1
|
Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
Collapse
Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
| |
Collapse
|
2
|
Lin C, Mazor Y, Reppert M. Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis. J Phys Chem B 2024; 128:2266-2280. [PMID: 38442033 DOI: 10.1021/acs.jpcb.3c06488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.
Collapse
Affiliation(s)
- Chientzu Lin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| | - Yuval Mazor
- School of Molecular Sciences, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47920, United States
| |
Collapse
|
3
|
Ivanova AD, Kotova DA, Khramova YV, Morozova KI, Serebryanaya DV, Bochkova ZV, Sergeeva AD, Panova AS, Katrukha IA, Moshchenko AA, Oleinikov VA, Semyanov AV, Belousov VV, Katrukha AG, Brazhe NA, Bilan DS. Redox differences between rat neonatal and adult cardiomyocytes under hypoxia. Free Radic Biol Med 2024; 211:145-157. [PMID: 38043869 DOI: 10.1016/j.freeradbiomed.2023.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
It is generally accepted that oxidative stress plays a key role in the development of ischemia-reperfusion injury in ischemic heart disease. However, the mechanisms how reactive oxygen species trigger cellular damage are not fully understood. Our study investigates redox state and highly reactive substances within neonatal and adult cardiomyocytes under hypoxia conditions. We have found that hypoxia induced an increase in H2O2 production in adult cardiomyocytes, while neonatal cardiomyocytes experienced a decrease in H2O2 levels. This finding correlates with our observation of the difference between the electron transport chain (ETC) properties and mitochondria amount in adult and neonatal cells. We demonstrated that in adult cardiomyocytes hypoxia caused the significant increase in the ETC loading with electrons compared to normoxia. On the contrary, in neonatal cardiomyocytes ETC loading with electrons was similar under both normoxic and hypoxic conditions that could be due to ETC non-functional state and the absence of the electrons transfer to O2 under normoxia. In addition to the variations in H2O2 production, we also noted consistent pH dynamics under hypoxic conditions. Notably, the pH levels exhibited a similar decrease in both cell types, thus, acidosis is a more universal cellular response to hypoxia. We also demonstrated that the amount of mitochondria and the levels of cardiac isoforms of troponin I, troponin T, myoglobin and GAPDH were significantly higher in adult cardiomyocytes compared to neonatal ones. Remarkably, we found out that under hypoxia, the levels of cardiac isoforms of troponin T, myoglobin, and GAPDH were elevated in adult cardiomyocytes, while their level in neonatal cells remained unchanged. Obtained data contribute to the understanding of the mechanisms of neonatal cardiomyocytes' resistance to hypoxia and the ability to maintain the metabolic homeostasis in contrast to adult ones.
Collapse
Affiliation(s)
- Alexandra D Ivanova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Daria A Kotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Yulia V Khramova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ksenia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Daria V Serebryanaya
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Zhanna V Bochkova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anastasia D Sergeeva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anastasiya S Panova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Ivan A Katrukha
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Aleksandr A Moshchenko
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Vladimir A Oleinikov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; National Research Nuclear University Moscow Engineering Physics Institute, Moscow, 115409, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Alexey G Katrukha
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
| |
Collapse
|
4
|
Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
Collapse
Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| |
Collapse
|
5
|
Auerbach H, Faus I, Rackwitz S, Wolny JA, Chumakov AI, Knipp M, Walker FA, Schünemann V. Heme protonation affects iron-NO binding in the NO transport protein nitrophorin. J Inorg Biochem 2023; 246:112281. [PMID: 37352657 DOI: 10.1016/j.jinorgbio.2023.112281] [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: 01/31/2023] [Revised: 04/26/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
The nitrophorins (NPs) comprise an unusual group of heme proteins with stable ferric heme iron nitric oxide (Fe-NO) complexes. They are found in the salivary glands of the blood-sucking kissing bug Rhodnius prolixus, which uses the NPs to transport the highly reactive signaling molecule NO. Nuclear resonance vibrational spectroscopy (NRVS) of both isoform NP2 and a mutant NP2(Leu132Val) show, after addition of NO, a strong structured vibrational band at around 600 cm-1, which is due to modes with significant Fe-NO bending and stretching contribution. Based on a hybrid calculation method, which uses density functional theory and molecular mechanics, it is demonstrated that protonation of the heme carboxyl groups does influence both the vibrational properties of the Fe-NO entity and its electronic ground state. Moreover, heme protonation causes a significant increase of the gap between the highest occupied and lowest unoccupied molecular orbital by almost one order of magnitude leading to a stabilization of the Fe-NO bond.
Collapse
Affiliation(s)
- Hendrik Auerbach
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Isabelle Faus
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Sergej Rackwitz
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Juliusz A Wolny
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | | | - Markus Knipp
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany; Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - F Ann Walker
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721-0041, United States
| | - Volker Schünemann
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany.
| |
Collapse
|
6
|
Gonçalves Dalkiranis G, Costa Basílio F, Nobuyasu RS, de Fátima Curcino da Silva S, Lucia Dias Nogueira S, Moreira Therézio E, Serein-Spirau F, Silva RA, Marletta A. Photoluminescent ellipsometric circular dichroism. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 293:122437. [PMID: 36758363 DOI: 10.1016/j.saa.2023.122437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/11/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
A novel spectroscopic technique, photoluminescent ellipsometric circular dichroism (PECD), which distinguishes all radiative electronic transitions related to molecular chiral centers. Additionally, it is proposed as complementary to the ellipsometric Raman spectroscopy (ERS) technique, thus establishing a relationship between vibrational modes and electronic transitions, associated with molecular chiral centers. In this way, PECD turns into a powerful technique for chiral material characterization. The PECD technique was performed on a chiral oligomer (1R,2R)-diiminocyclohexane, and its derivative polymer. A complete photophysical characterization in solution was performed to corroborate the new PECD technique.
Collapse
Affiliation(s)
- Gustavo Gonçalves Dalkiranis
- Physics Institute of São Carlos, University of São Paulo, 13560-970 São Carlos, SP, Brazil; Catalan Institute of Nanoscience and Nanotechnology (ICN2), Edifici ICN2, Campus UAB, 08193, Bellaterra, Barcelona, Spain.
| | | | - Roberto S Nobuyasu
- Physics and Chemistry Institute, Federal University of Itajubá, CEP 37500-903 Itajubá, MG, Brazil
| | | | | | | | - Françoise Serein-Spirau
- Institut Charles Gerhardt, Ecole Nationale Superieure de Chimie de Montpellier, 34296 Montpellier, France
| | - Raigna A Silva
- Physics Institute, Federal University of Uberlândia, 38400-902 Uberlândia, MG, Brazil
| | - Alexandre Marletta
- Physics Institute, Federal University of Uberlândia, 38400-902 Uberlândia, MG, Brazil
| |
Collapse
|
7
|
Brazhe NA, Nikelshparg EI, Baizhumanov AA, Grivennikova VG, Semenova AA, Novikov SM, Volkov VS, Arsenin AV, Yakubovsky DI, Evlyukhin AB, Bochkova ZV, Goodilin EA, Maksimov GV, Sosnovtseva O, Rubin AB. SERS uncovers the link between conformation of cytochrome c heme and mitochondrial membrane potential. Free Radic Biol Med 2023; 196:133-144. [PMID: 36649901 DOI: 10.1016/j.freeradbiomed.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
The balance between the mitochondrial respiratory chain activity and the cell's needs in ATP ensures optimal cellular function. Cytochrome c is an essential component of the electron transport chain (ETC), which regulates ETC activity, oxygen consumption, ATP synthesis and can initiate apoptosis. The impact of conformational changes in cytochrome c on its function is not understood for the lack of access to these changes in intact mitochondria. We have developed a novel sensor that uses unique properties of label-free surface-enhanced Raman spectroscopy (SERS) to identify conformational changes in heme of cytochrome c and to elucidate their role in functioning mitochondria. We have verified that molecule bond vibrations assessed by SERS are a reliable indicator of the heme conformation during changes in the inner mitochondrial membrane potential and ETC activity. We have demonstrated that cytochrome c heme reversibly switches between planar and ruffled conformations in response to the inner mitochondrial membrane potential (ΔΨ) and H+ concentration in the intermembrane space. This regulates the efficiency of the mitochondrial respiratory chain, thus, adjusting the mitochondrial respiration to the cell's consumption of ATP and the overall activity. We have found that under hypertensive conditions cytochrome c heme loses its sensitivity to ΔΨ that can affect the regulation of ETC activity. The ability of the proposed SERS-based sensor to track mitochondrial function opens broad perspectives in cell bioenergetics.
Collapse
Affiliation(s)
- Nadezda A Brazhe
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia.
| | - Evelina I Nikelshparg
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| | - Adil A Baizhumanov
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| | - Vera G Grivennikova
- Department of Biochemistry, Biological Faculty, Moscow State University, 119234, Russia
| | - Anna A Semenova
- Faculty of Materials Sciences, Moscow State University, 119899, Russia
| | - Sergey M Novikov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia
| | - Valentyn S Volkov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia; GrapheneTek, Skolkovo Innovation Center, Moscow, 121205, Russia
| | - Aleksey V Arsenin
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia
| | - Dmitry I Yakubovsky
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology, 141701, Russia
| | - Andrey B Evlyukhin
- Institute of Quantum Optics, Leibniz Universität Hannover, Hannover, 30167, Germany
| | - Zhanna V Bochkova
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| | - Eugene A Goodilin
- Faculty of Materials Sciences, Moscow State University, 119899, Russia; Faculty of Chemistry, Moscow State University, 119991, Russia; Kurnakov Institute of General and Inorganic Chemistry RAS, Moscow, 119071, Russia
| | - Georgy V Maksimov
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia; Federal State Autonomous Educational Institution of Higher Education "National Research Technological University "MISiS", Moscow, 119049, Russia
| | - Olga Sosnovtseva
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK, 2200, Denmark.
| | - Andrey B Rubin
- Department of Biophysics, Biological Faculty, Moscow State University, 119234, Russia
| |
Collapse
|
8
|
Kondo HX, Iizuka H, Masumoto G, Kabaya Y, Kanematsu Y, Takano Y. Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network. Biomolecules 2023; 13:biom13010137. [PMID: 36671521 PMCID: PMC9855806 DOI: 10.3390/biom13010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Structure-function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure-function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure-function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB-OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with quite different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure-function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.
Collapse
Affiliation(s)
- Hiroko X. Kondo
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita 565-0874, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
| | - Hiroyuki Iizuka
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14, Nishi 9, Kitaku, Sapporo 060-0814, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Information R&D and Strategy Headquarters, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yuichi Kabaya
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yusuke Kanematsu
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
| |
Collapse
|
9
|
Absolute excited state molecular geometries revealed by resonance Raman signals. Nat Commun 2022; 13:7770. [PMID: 36522323 PMCID: PMC9755279 DOI: 10.1038/s41467-022-35099-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Ultrafast reactions activated by light absorption are governed by multidimensional excited-state (ES) potential energy surfaces (PESs), which describe how the molecular potential varies with the nuclear coordinates. ES PESs ad-hoc displaced with respect to the ground state can drive subtle structural rearrangements, accompanying molecular biological activity and regulating physical/chemical properties. Such displacements are encoded in the Franck-Condon overlap integrals, which in turn determine the resonant Raman response. Conventional spectroscopic approaches only access their absolute value, and hence cannot determine the sense of ES displacements. Here, we introduce a two-color broadband impulsive Raman experimental scheme, to directly measure complex Raman excitation profiles along desired normal modes. The key to achieve this task is in the signal linear dependence on the Frank-Condon overlaps, brought about by non-degenerate resonant probe and off-resonant pump pulses, which ultimately enables time-domain sensitivity to the phase of the stimulated vibrational coherences. Our results provide the tool to determine the magnitude and the sensed direction of ES displacements, unambiguously relating them to the ground state eigenvectors reference frame.
Collapse
|
10
|
Olloqui-Sariego JL, Pérez-Mejías G, Márquez I, Guerra-Castellano A, Calvente JJ, De la Rosa MA, Andreu R, Díaz-Moreno I. Electric field-induced functional changes in electrode-immobilized mutant species of human cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148570. [PMID: 35643148 DOI: 10.1016/j.bbabio.2022.148570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/21/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Post-translational modifications and naturally occurring mutations of cytochrome c have been recognized as a regulatory mechanism to control its biology. In this work, we investigate the effect of such in vivo chemical modifications of human cytochrome c on its redox properties in the adsorbed state onto an electrode. In particular, tyrosines 48 and 97 have been replaced by the non-canonical amino acid p-carboxymethyl-L-phenylalanine (pCMF), thus mimicking tyrosine phosphorylation. Additionally, tyrosine 48 has been replaced by a histidine producing the natural Y48H pathogenic mutant. Thermodynamics and kinetics of the interfacial electron transfer of wild-type cytochrome c and herein produced variants, adsorbed electrostatically under different local interfacial electric fields, were determined by means of variable temperature cyclic film voltammetry. It is shown that non-native cytochrome c variants immobilized under a low interfacial electric field display redox thermodynamics and kinetics similar to those of wild-type cytochrome c. However, upon increasing the strength of the electric field, the redox thermodynamics and kinetics of the modified proteins markedly differ from those of the wild-type species. The mutations promote stabilization of the oxidized form and a significant increase in the activation enthalpy values that can be ascribed to a subtle distortion of the heme cofactor and/or difference of the amino acid rearrangements rather than to a coarse protein structural change. Overall, these results point to a combined effect of the single point mutations at positions 48 and 97 and the strength of electrostatic binding on the regulatory mechanism of mitochondrial membrane activity, when acting as a redox shuttle protein.
Collapse
Affiliation(s)
- José Luis Olloqui-Sariego
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Inmaculada Márquez
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain; Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Juan José Calvente
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Rafael Andreu
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain).
| |
Collapse
|
11
|
Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network. Biomolecules 2022; 12:biom12091172. [PMID: 36139011 PMCID: PMC9496533 DOI: 10.3390/biom12091172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Heme proteins serve diverse and pivotal biological functions. Therefore, clarifying the mechanisms of these diverse functions of heme is a crucial scientific topic. Distortion of heme porphyrin is one of the key factors regulating the chemical properties of heme. Here, we constructed convolutional neural network models for predicting heme distortion from the tertiary structure of the heme-binding pocket to examine their correlation. For saddling, ruffling, doming, and waving distortions, the experimental structure and predicted values were closely correlated. Furthermore, we assessed the correlation between the cavity shape and molecular structure of heme and demonstrated that hemes in protein pockets with similar structures exhibit near-identical structures, indicating the regulation of heme distortion through the protein environment. These findings indicate that the tertiary structure of the heme-binding pocket is one of the factors regulating the distortion of heme porphyrin, thereby controlling the chemical properties of heme relevant to the protein function; this implies a structure–function correlation in heme proteins.
Collapse
|
12
|
Dahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O’Brien JP, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. SCIENCE ADVANCES 2022; 8:eabm7193. [PMID: 35544567 PMCID: PMC9094664 DOI: 10.1126/sciadv.abm7193] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/28/2022] [Indexed: 06/10/2023]
Abstract
Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>1010 s-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.
Collapse
Affiliation(s)
- Peter J. Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sophia M. Yi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Yangqi Gu
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Catharine Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jens Neu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - J. Patrick O’Brien
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Matthew J. Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Dennis Vu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | | | - Nikhil S. Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| |
Collapse
|
13
|
Chertkova RV, Firsov AM, Brazhe NA, Nikelshparg EI, Bochkova ZV, Bryantseva TV, Semenova MA, Baizhumanov AA, Kotova EA, Kirpichnikov MP, Maksimov GV, Antonenko YN, Dolgikh DA. Multiple Mutations in the Non-Ordered Red Ω-Loop Enhance the Membrane-Permeabilizing and Peroxidase-like Activity of Cytochrome c. Biomolecules 2022; 12:biom12050665. [PMID: 35625593 PMCID: PMC9138828 DOI: 10.3390/biom12050665] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 02/04/2023] Open
Abstract
A key event in the cytochrome c-dependent apoptotic pathway is the permeabilization of the outer mitochondrial membrane, resulting in the release of various apoptogenic factors, including cytochrome c, into the cytosol. It is believed that the permeabilization of the outer mitochondrial membrane can be induced by the peroxidase activity of cytochrome c in a complex with cardiolipin. Using a number of mutant variants of cytochrome c, we showed that both substitutions of Lys residues from the universal binding site for oppositely charged Glu residues and mutations leading to a decrease in the conformational mobility of the red Ω-loop in almost all cases did not affect the ability of cytochrome c to bind to cardiolipin. At the same time, the peroxidase activity of all mutant variants in a complex with cardiolipin was three to five times higher than that of the wild type. A pronounced increase in the ability to permeabilize the lipid membrane in the presence of hydrogen peroxide, as measured by calcein leakage from liposomes, was observed only in the case of four substitutions in the red Ω-loop (M4 mutant). According to resonance and surface-enhanced Raman spectroscopy, the mutations caused significant changes in the heme of oxidized cytochrome c molecules resulting in an increased probability of the plane heme conformation and the enhancement of the rigidity of the protein surrounding the heme. The binding of wild-type and mutant forms of oxidized cytochrome c to cardiolipin-containing liposomes caused the disordering of the acyl lipid chains that was more pronounced for the M4 mutant. Our findings indicate that the Ω-loop is important for the pore formation in cardiolipin-containing membranes.
Collapse
Affiliation(s)
- Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Correspondence: (R.V.C.); (N.A.B.)
| | - Alexander M. Firsov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (E.A.K.); (Y.N.A.)
| | - Nadezda A. Brazhe
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
- Correspondence: (R.V.C.); (N.A.B.)
| | - Evelina I. Nikelshparg
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Zhanna V. Bochkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Tatyana V. Bryantseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Marina A. Semenova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
| | - Adil A. Baizhumanov
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
| | - Elena A. Kotova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (E.A.K.); (Y.N.A.)
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Georgy V. Maksimov
- Biophysics Department, Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.I.N.); (A.A.B.); (G.V.M.)
- Federal State Autonomous Educational Institution of Higher Education “National Research Technological University “MISiS””, 119049 Moscow, Russia
| | - Yuriy N. Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (A.M.F.); (E.A.K.); (Y.N.A.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (Z.V.B.); (T.V.B.); (M.A.S.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, 119899 Moscow, Russia
| |
Collapse
|
14
|
Redox state changes of mitochondrial cytochromes in brain and breast cancers by Raman spectroscopy and imaging. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132134] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
15
|
Kondo HX, Fujii M, Tanioka T, Kanematsu Y, Yoshida T, Takano Y. Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. J Chem Inf Model 2022; 62:775-784. [PMID: 35157473 DOI: 10.1021/acs.jcim.1c01315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis to oxygen transport and/or storage. Although the distortion of heme porphyrin correlates with the physical properties of heme, such as the redox potential and oxygen affinity, the relationship between heme distortion and the heme protein environment is unclear. Here, we tested the hypothesis that the protein environment of the heme-binding pocket determines heme distortion (conformation). We analyzed the correlations between the amino acid composition of the heme-binding pocket and the magnitude of heme distortion along 12 vibrational modes using machine learning. A correlation was detected in the three lowest vibrational modes. Analysis of heme distortions in nearly the same environments of the heme-binding pocket supported this notion. Our analyses indicate that the heme-binding pocket environment is a major factor impacting the distortion of heme porphyrin along the three lowest vibrational modes. In addition, statistical analysis of the distortion of heme porphyrin revealed that the peaks of distributions of the ruffling and breathing distortions are shifted from 0 (the equilibrium structure). Both the ruffling and breathing distortions are correlated with the redox potential of heme, so that heme molecules with these distortions have a lower redox potential than planar molecules. These findings explain the structure-function relationship of heme.
Collapse
Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan.,Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Masanori Fujii
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Takuma Tanioka
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takashi Yoshida
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
| |
Collapse
|
16
|
Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin. Life (Basel) 2022; 12:life12020210. [PMID: 35207496 PMCID: PMC8880375 DOI: 10.3390/life12020210] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physical properties of heme, such as oxygen affinity and redox potential. Therefore, clarification of the relationship between heme distortion and the protein environment is crucial in protein science. Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations as well as statistical analysis of the protein structures of hemoglobin and myoglobin stored in Protein Data Bank. Our computation and statistical analysis showed that the protein environment for hemoglobin and myoglobin prominently affects the doming distortion of heme porphyrin, which correlates with its oxygen affinity, and that the magnitude of distortion is different between hemoglobin and myoglobin. These results suggest that heme distortion is affected by its protein environment and fluctuates around its fitted conformation, leading to physical properties that are appropriate for protein functions.
Collapse
|
17
|
Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
18
|
Batignani G, Sansone C, Ferrante C, Fumero G, Mukamel S, Scopigno T. Excited-State Energy Surfaces in Molecules Revealed by Impulsive Stimulated Raman Excitation Profiles. J Phys Chem Lett 2021; 12:9239-9247. [PMID: 34533307 PMCID: PMC8488957 DOI: 10.1021/acs.jpclett.1c02209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/16/2021] [Indexed: 05/14/2023]
Abstract
Photophysical and photochemical processes are ruled by the interplay between transient vibrational and electronic degrees of freedom, which are ultimately determined by the multidimensional potential energy surfaces (PESs). Differences between ground and excited PESs are encoded in the relative intensities of resonant Raman bands, but they are experimentally challenging to access, requiring measurements at multiple wavelengths under identical conditions. Herein, we perform a two-color impulsive vibrational scattering experiment to launch nuclear wavepacket motions by an impulsive pump and record their coupling with a targeted excited-state potential by resonant Raman processes with a delayed probe, generating in a single measurement background-free vibrational spectra across the entire sample absorption. Building on the interference between the multiple pathways resonant with the excited-state manifold that generate the Raman signal, we show how to experimentally tune their relative phase by varying the probe chirp, decoding nuclear displacements along different normal modes and revealing the multidimensional PESs. Our results are validated against time-dependent density functional theory.
Collapse
Affiliation(s)
- Giovanni Batignani
- Dipartimento
di Fisica, Universitá di Roma “La
Sapienza”, Roma I-00185, Italy
- Istituto
Italiano di Tecnologia, Center for Life Nano Science @Sapienza, Roma I-00161, Italy
| | - Carlotta Sansone
- Dipartimento
di Fisica, Universitá di Roma “La
Sapienza”, Roma I-00185, Italy
| | - Carino Ferrante
- Dipartimento
di Fisica, Universitá di Roma “La
Sapienza”, Roma I-00185, Italy
- Istituto
Italiano di Tecnologia, Center for Life Nano Science @Sapienza, Roma I-00161, Italy
| | - Giuseppe Fumero
- Dipartimento
di Fisica, Universitá di Roma “La
Sapienza”, Roma I-00185, Italy
| | - Shaul Mukamel
- Department
of Chemistry, University of California, Irvine, California 92623, United States
| | - Tullio Scopigno
- Dipartimento
di Fisica, Universitá di Roma “La
Sapienza”, Roma I-00185, Italy
- Istituto
Italiano di Tecnologia, Center for Life Nano Science @Sapienza, Roma I-00161, Italy
| |
Collapse
|
19
|
Slatinskaya OV, Luneva OG, Deev LI, Zaripov PI, Maksimov GV. The Hemoglobin Conformation in Erythrocytes at Different Levels of Oxygen Partial Pressure. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921050225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
20
|
Amino Acid Substitutions in the Non-Ordered Ω-Loop 70–85 Affect Electron Transfer Function and Secondary Structure of Mitochondrial Cytochrome c. CRYSTALS 2021. [DOI: 10.3390/cryst11080973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The secondary structure of horse cytochrome c with mutations in the P76GTKMIFA83 site of the Ω-loop, exhibiting reduced efficiency of electron transfer, were studied. CD spectroscopy studies showed that the ordering of mutant structure increases by 3–6% compared to that of the WT molecules due to the higher content of β-structural elements. The IR spectroscopy data are consistent with the CD results and demonstrate that some α-helical elements change into β-structures, and the amount of the non-structured elements is decreased. The analysis of the 1H-NMR spectra demonstrated that cytochrome c mutants have a well-determined secondary structure with some specific features related to changes in the heme microenvironment. The observed changes in the structure of cytochrome c mutants are likely to be responsible for the decrease in the conformational mobility of the P76GTKMIFA83 sequence carrying mutations and for the decline in succinate:cytochrome c-reductase and cytochrome c-oxidase activities in the mitoplast system in the presence of these cytochromes c. We suggest that the decreased efficiency of the electron transfer of the studied cytochromes c may arise due to: (1) the change in the protein conformation in sites responsible for the interaction of cytochrome c with complexes III and IV and (2) the change in the heme conformation that deteriorates its optimal orientation towards donor and acceptor in complexes III and IV therefore slows down electron transfer. The results obtained are consistent with the previously proposed model of mitochondrial cytochrome c functioning associated with the deterministic mobility of protein globule parts.
Collapse
|
21
|
Ferousi C, Schmitz RA, Maalcke WJ, Lindhoud S, Versantvoort W, Jetten MSM, Reimann J, Kartal B. Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link. J Biol Chem 2021; 296:100476. [PMID: 33652023 PMCID: PMC8042395 DOI: 10.1016/j.jbc.2021.100476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.
Collapse
Affiliation(s)
- Christina Ferousi
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter J Maalcke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| |
Collapse
|
22
|
Cheng C, Hayashi S. Ab Initio Evaluation of the Redox Potential of Cytochrome c. J Chem Theory Comput 2021; 17:1194-1207. [PMID: 33459006 DOI: 10.1021/acs.jctc.0c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various biochemical activities of metabolism and biosynthesis are fulfilled by redox processes with explicit electron exchange, which furnish redox enzymes with high chemical reactivity. However, theoretical investigation of a redox process, which simultaneously involves a complex electronic change at a redox metal center and conformational reorganization of the surrounding protein environment coupled to the electronic change, requires computationally conflicting approaches, highly accurate quantum chemical calculations, and long-time molecular dynamics (MD) simulations, limiting the physicochemical understanding of biological redox processes. Here, we theoretically examined a redox process of cytochrome c by means of a hybrid molecular simulation technique, which enables one to consistently treat the redox center at the ab initio quantum chemistry level of theory and the protein reorganization with long-time MD simulations on the microsecond timescale. The calculations successfully evaluated a large absolute redox potential, 4.34 eV, with errors of only 0.03 to 0.34 eV to the experimental ones without any problem-specific empirical parameters. Through the long-time MD sampling, large and nonlinear reorganization of the protein environment was unveiled and the molecular determinants for the redox potential were identified. The present ab initio approach significantly expands the applicability of theoretical investigation to biological redox systems with more electronically complicated redox centers such as polynuclear transition metal complexes.
Collapse
Affiliation(s)
- Cheng Cheng
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
23
|
Roos G, Harvey JN. Histidine versus Cysteine-Bearing Heme-Dependent Halogen Peroxidases: Parallels and Differences for Cl - Oxidation. J Phys Chem B 2021; 125:74-85. [PMID: 33350832 DOI: 10.1021/acs.jpcb.0c09409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homodimeric myeloperoxidase (MPO) features a histidine as a proximal ligand and a sulfonium linkage covalently attaching the heme porphyrin ring to the protein. MPO is able to catalyze Cl- oxidation with about the same efficiency as chloroperoxidase at pH 7.0. In this study, we seek to explore the parallels and differences between the histidine and cysteine heme-dependent halogen peroxidases. Transition states, reaction barriers, and relevant thermodynamic properties are calculated on protein models. Together with electronic structure calculations, it gives an overview of the reaction mechanisms and of the factors that determine the selectivity between one- and two-electron paths. Conclusions point to the innate oxidizing nature of MPO with the ester and sulfonium linkages hiking up the reactivity to enable chloride oxidation. The installation of a deprotonated imidazolate as a proximal ligand does not shift the equilibrium from one- to two-electron events without influencing the chemistry of the oxidation reaction.
Collapse
Affiliation(s)
- Goedele Roos
- UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, CNRS, UMR 8576, F-59000 Lille, France
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| |
Collapse
|
24
|
Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
Collapse
|
25
|
Kondo HX, Kanematsu Y, Masumoto G, Takano Y. PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins. Database (Oxford) 2020; 2023:baaa066. [PMID: 33002111 PMCID: PMC10755257 DOI: 10.1093/database/baaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 11/14/2022]
Abstract
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure-function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/.
Collapse
Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita 565-0874, Japan and
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Head Office for Information Systems and Cybersecurity, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
| |
Collapse
|
26
|
Bacellar C, Kinschel D, Mancini GF, Ingle RA, Rouxel J, Cannelli O, Cirelli C, Knopp G, Szlachetko J, Lima FA, Menzi S, Pamfilidis G, Kubicek K, Khakhulin D, Gawelda W, Rodriguez-Fernandez A, Biednov M, Bressler C, Arrell CA, Johnson PJM, Milne CJ, Chergui M. Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies. Proc Natl Acad Sci U S A 2020; 117:21914-21920. [PMID: 32848065 PMCID: PMC7486745 DOI: 10.1073/pnas.2009490117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structure-function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kβ X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.
Collapse
Affiliation(s)
- Camila Bacellar
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Dominik Kinschel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giulia F Mancini
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca A Ingle
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jérémy Rouxel
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Oliviero Cannelli
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Claudio Cirelli
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Jakub Szlachetko
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Kraków, Poland
| | | | - Samuel Menzi
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Georgios Pamfilidis
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | | | | | - Wojciech Gawelda
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland
| | | | - Mykola Biednov
- European X-ray Free Electron Laser, D-22869 Schenefeld, Germany
| | | | - Christopher A Arrell
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Christopher J Milne
- Swiss Free Electron Laser, Paul-Scherrer-Institut (PSI), 5232 Villigen PSI, Switzerland
| | - Majed Chergui
- Laboratoire de Spectroscopie Ultrarapide, Institut des Sciences et Ingéniéries Chimiques and Lausanne Centre for Ultrafast Science, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
| |
Collapse
|
27
|
Coleman RE, Vilbert AC, Lancaster KM. The Heme-Lys Cross-Link in Cytochrome P460 Promotes Catalysis by Enforcing Secondary Coordination Sphere Architecture. Biochemistry 2020; 59:2289-2298. [PMID: 32525655 DOI: 10.1021/acs.biochem.0c00261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome (cyt) P460 is a c-type monoheme enzyme found in ammonia-oxidizing bacteria (AOB) and methanotrophs; additionally, genes encoding it have been found in some pathogenic bacteria. Cyt P460 is defined by a unique post-translational modification to the heme macrocycle, where a lysine (Lys) residue covalently attaches to the 13' meso carbon of the porphyrin, modifying this heme macrocycle into the enzyme's eponymous P460 cofactor, similar to the cofactor found in the enzyme hydroxylamine oxidoreductase. This cross-link imbues the protein with unique spectroscopic properties, the most obvious of which is the enzyme's green color in solution. Cyt P460 from the AOB Nitrosomonas europaea is a homodimeric redox enzyme that produces nitrous oxide (N2O) from 2 equiv of hydroxylamine. Mutation of the Lys cross-link results in spectroscopic features that are more similar to those of standard cyt c' proteins and renders the enzyme catalytically incompetent for NH2OH oxidation. Recently, the necessity of a second-sphere glutamate (Glu) residue for redox catalysis was established; it plausibly serves as proton relay during the first oxidative half of the catalytic cycle. Herein, we report the first crystal structure of a cross-link deficient cyt P460. This structure shows that the positioning of the catalytically essential Glu changes by approximately 0.8 Å when compared to a cross-linked, catalytically competent cyt P460. It appears that the heme-Lys cross-link affects the relative position of the P460 cofactor with respect to the second-sphere Glu residue, therefore dictating the catalytic competency of the enzyme.
Collapse
Affiliation(s)
- Rachael E Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Avery C Vilbert
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
28
|
Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
Collapse
Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
| |
Collapse
|
29
|
From Synthesis to Utilization: The Ins and Outs of Mitochondrial Heme. Cells 2020; 9:cells9030579. [PMID: 32121449 PMCID: PMC7140478 DOI: 10.3390/cells9030579] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 12/14/2022] Open
Abstract
Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria.
Collapse
|
30
|
Ferrante C, Batignani G, Pontecorvo E, Montemiglio LC, Vos MH, Scopigno T. Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy. J Am Chem Soc 2020; 142:2285-2292. [PMID: 31917551 PMCID: PMC7735705 DOI: 10.1021/jacs.9b10560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Identifying
the structural rearrangements during photoinduced reactions is a fundamental
challenge for understanding from a microscopic perspective the dynamics
underlying the functional mechanisms of heme proteins. Here, femtosecond
stimulated Raman spectroscopy is applied to follow the ultrafast evolution
of two different proteins, each bearing a six-coordinate heme with
two amino acid axial ligands. By exploiting the sensitivity of Raman
spectra to the structural configuration, we investigate the effects
of photolysis and the binding of amino acid residues in cytochrome c and neuroglobin. By comparing the system response for
different time delays and Raman pump resonances, we show how detailed
properties of atomic motions and energy redistribution can be unveiled.
In particular, we demonstrate substantially faster energy flow from
the dissociated heme to the protein moiety in cytochrome c, which we assign to the presence of covalent heme–protein
bonds.
Collapse
Affiliation(s)
- Carino Ferrante
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
| | | | | | | | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Tullio Scopigno
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
| |
Collapse
|
31
|
Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
Collapse
|
32
|
Paquete CM, Rusconi G, Silva AV, Soares R, Louro RO. A brief survey of the "cytochromome". Adv Microb Physiol 2019; 75:69-135. [PMID: 31655743 DOI: 10.1016/bs.ampbs.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.
Collapse
|
33
|
Bacon BA, Liu Y, Kincaid JR, Boon EM. Spectral Characterization of a Novel NO Sensing Protein in Bacteria: NosP. Biochemistry 2018; 57:6187-6200. [PMID: 30272959 DOI: 10.1021/acs.biochem.8b00451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A novel family of bacterial hemoproteins named NosP has been discovered recently; its members are proposed to function as nitric oxide (NO) responsive proteins involved in bacterial group behaviors such as quorum sensing and biofilm growth and dispersal. Currently, little is known about molecular activation mechanisms in NosP. Here, functional studies were performed utilizing the distinct spectroscopic characteristics associated with the NosP heme cofactor. NosPs from Pseudomonas aeruginosa ( Pa), Vibrio cholerae ( Vc), and Legionella pneumophila ( Lpg) were studied in their ferrous unligated forms as well as their ferrous CO, ferrous NO, and ferric CN adducts. The resonance Raman (rR) data collected on the ferric forms strongly support the existence of a distorted heme cofactor, which is a common feature in NO sensors. The ferrous spectra exhibit a 213 cm-1 feature, which is assigned to the Fe-Nhis stretching mode. The Fe-C and C-O frequencies in the spectra of ferrous CO NosP complexes are inversely correlated with relatively similar frequencies, consistent with a proximal histidine ligand and a relatively hydrophobic environment. The rR spectra obtained for isotopically labeled ferrous NO adducts provide evidence of formation of a 5-coordinate NO complex, resulting from proximal Fe-Nhis cleavage, which is believed to play a role in biological heme-NO signal transduction. Additionally, we found that of the three NosPs studied, Lpg NosP contains the most electropositive ligand binding pocket, while Pa NosP has the most electronegative ligand binding pocket. This pattern is also observed in the measured heme reduction potentials for these three proteins, which may indicate distinct functions for each.
Collapse
Affiliation(s)
- Bezalel A Bacon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States
| | - Yilin Liu
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - James R Kincaid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Elizabeth M Boon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States.,Department of Chemistry and Institute of Chemical Biology and Drug Discovery , Stony Brook University , Stony Brook , New York 11794-3400 , United States
| |
Collapse
|
34
|
Kanematsu Y, Kondo HX, Imada Y, Takano Y. Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
35
|
Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
Collapse
|
36
|
Malyshka D, Schweitzer-Stenner R. Photoreduction of ferricytochrome c in the presence of potassium ferrocyanide. Photochem Photobiol Sci 2018; 17:1462-1468. [DOI: 10.1039/c8pp00286j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferricytochrome c has been previously shown to photoreduce in the presence of ferrocyanide anions, but the process has been poorly understood.
Collapse
|
37
|
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
| |
Collapse
|
38
|
Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| |
Collapse
|
39
|
Imada Y, Nakamura H, Takano Y. Density functional study of porphyrin distortion effects on redox potential of heme. J Comput Chem 2017; 39:143-150. [DOI: 10.1002/jcc.25058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/29/2017] [Accepted: 08/18/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Yasuhiro Imada
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Haruki Nakamura
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka; Suita Osaka 565-0871 Japan
| | - Yu Takano
- Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, 3-2 Yamadaoka; Suita Osaka 565-0871 Japan
- Department of Biomedical Information Sciences; Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku; Hiroshima 731-3194 Japan
| |
Collapse
|
40
|
Alvarez-Paggi D, Zitare UA, Szuster J, Morgada MN, Leguto AJ, Vila AJ, Murgida DH. Tuning of Enthalpic/Entropic Parameters of a Protein Redox Center through Manipulation of the Electronic Partition Function. J Am Chem Soc 2017; 139:9803-9806. [PMID: 28662578 DOI: 10.1021/jacs.7b05199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Manipulation of the partition function (Q) of the redox center CuA from cytochrome c oxidase is attained by tuning the accessibility of a low lying alternative electronic ground state and by perturbation of the electrostatic potential through point mutations, loop engineering and pH variation. We report clear correlations of the entropic and enthalpic contributions to redox potentials with Q and with the identity and hydrophobicity of the weak axial ligand, respectively.
Collapse
Affiliation(s)
- Damian Alvarez-Paggi
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| | - Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET , 2000 Rosario, Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET , 2000 Rosario, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET , 2000 Rosario, Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Milazzo L, Tognaccini L, Howes BD, Sinibaldi F, Piro MC, Fittipaldi M, Baratto MC, Pogni R, Santucci R, Smulevich G. Unravelling the Non-Native Low-Spin State of the Cytochrome c–Cardiolipin Complex: Evidence of the Formation of a His-Ligated Species Only. Biochemistry 2017; 56:1887-1898. [DOI: 10.1021/acs.biochem.6b01281] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lisa Milazzo
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Lorenzo Tognaccini
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Barry D. Howes
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Federica Sinibaldi
- Dipartimento
di Medicina Sperimentale e Chirurgia, Università di Roma “Tor Vergata”, Via
Montpellier 1, 00133 Rome, Italy
| | - Maria C. Piro
- Dipartimento
di Medicina Sperimentale e Chirurgia, Università di Roma “Tor Vergata”, Via
Montpellier 1, 00133 Rome, Italy
| | - Maria Fittipaldi
- Dipartimento
di Fisica ed Astronomia, Università di Firenze, Via Sansone
1, 50019 Sesto Fiorentino
(FI), Italy
| | - Maria C. Baratto
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro
2, 53100 Siena, Italy
| | - Rebecca Pogni
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro
2, 53100 Siena, Italy
| | - Roberto Santucci
- Dipartimento
di Scienze Cliniche e Medicina Traslazionale, Università di Roma “Tor Vergata”, Via
Montpellier 1, 00133 Rome, Italy
| | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
43
|
Hu J, Allen R, Rozinek S, Brancaleon L. Experimental and computational characterization of photosensitized conformational effects mediated by protoporphyrin ligands on human serum albumin. Photochem Photobiol Sci 2017; 16:694-710. [DOI: 10.1039/c6pp00096g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal-free and Zn-chelated protoporphyrins were bound to human serum albumin. Their binding parameters and locations were characterized and the effect of their irradiation on the conformation of the protein was demonstrated.
Collapse
Affiliation(s)
- Jie Hu
- Department of Physics and Astronomy
- University of Texas at San Antonio
- 78249 San Antonio
- USA
| | - Ryan Allen
- Department of Physics and Astronomy
- University of Texas at San Antonio
- 78249 San Antonio
- USA
| | - Sarah Rozinek
- Department of Physics and Astronomy
- University of Texas at San Antonio
- 78249 San Antonio
- USA
| | - Lorenzo Brancaleon
- Department of Physics and Astronomy
- University of Texas at San Antonio
- 78249 San Antonio
- USA
| |
Collapse
|
44
|
Kruglik SG, Yoo BK, Lambry JC, Martin JL, Negrerie M. Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states. Phys Chem Chem Phys 2017; 19:21317-21334. [DOI: 10.1039/c7cp02634j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After dissociation NO rebinds to Cyt c in 10 ps whereas Met80 rebinds in 5 μs after NO release from Cyt c. A complete view of heme – NO dynamics within 12 orders of magnitude of time in Cyt c is presented.
Collapse
Affiliation(s)
- Sergei G. Kruglik
- Laboratoire Jean Perrin
- Sorbonne Universités
- UPMC Univ. Paris 06
- CNRS
- 75005 Paris
| | - Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | | | - Jean-Louis Martin
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences
- INSERM
- Ecole Polytechnique
- 91128 Palaiseau
- France
| |
Collapse
|
45
|
Malyshka D, Schweitzer-Stenner R. Ferrocyanide-Mediated Photoreduction of Ferricytochrome C Utilized to Selectively Probe Non-native Conformations Induced by Binding to Cardiolipin-Containing Liposomes. Chemistry 2016; 23:1151-1156. [PMID: 27859757 DOI: 10.1002/chem.201604992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Indexed: 01/29/2023]
Abstract
Ferricytochrome c binding to cardiolipin-containing liposomes produces a heterogeneous distribution of conformations comprising native-like and non-native misfolded proteins. We utilized the photoreduction of native ferricytochrome c in the presence of potassium ferrocyanide and resonance Raman spectroscopy to probe the population of native and misfolded cytochrome c on liposomes with 20 % tetraoleylcardiolipin (TOCL)/80 % dioleylphosphocholine (DOPC) and with 100 % TOCL as a function of TOCL concentration. Our data provided strong support for an earlier model, which predicts that the equilibrium between native and non-native conformations is shifted to the latter with decreasing protein occupation of liposomes.
Collapse
Affiliation(s)
- Dmitry Malyshka
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | | |
Collapse
|
46
|
Zeng L, Wu L, Liu L, Jiang X. Analyzing Structural Properties of Heterogeneous Cardiolipin-Bound Cytochrome C and Their Regulation by Surface-Enhanced Infrared Absorption Spectroscopy. Anal Chem 2016; 88:11727-11733. [DOI: 10.1021/acs.analchem.6b03360] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Li Zeng
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lie Wu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Li Liu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiue Jiang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| |
Collapse
|
47
|
Bren KL. Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome
c. Isr J Chem 2016. [DOI: 10.1002/ijch.201600021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kara L. Bren
- Department of Chemistry University of Rochester Rochester NY 14627-0216 USA
| |
Collapse
|
48
|
Sun Y, Benabbas A, Zeng W, Muralidharan S, Boon EM, Champion PM. Kinetic Control of O2 Reactivity in H-NOX Domains. J Phys Chem B 2016; 120:5351-8. [PMID: 27229134 DOI: 10.1021/acs.jpcb.6b03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transient absorption, resonance Raman, and vibrational coherence spectroscopies are used to investigate the mechanisms of NO and O2 binding to WT Tt H-NOX and its P115A mutant. Vibrational coherence spectra of the oxy complexes provide clear evidence for the enhancement of an iron-histidine mode near 217 cm(-1) following photoexcitation, which indicates that O2 can be dissociated in these proteins. However, the quantum yield of O2 photolysis is low, particularly in the wild type (≲3%). Geminate recombination of O2 and NO in both of these proteins is very fast (∼1.4 × 10(11) s(-1)) and highly efficient. We show that the distal heme pocket of the H-NOX system forms an efficient trap that limits the O2 off-rate and determines the overall affinity. The distal pocket hydrogen bond, which appears to be stronger in the P115A mutant, may help retard the O2 ligand from escaping into the solvent following either photoinduced or thermal dissociation. This, along with a strengthening of the Fe-O2 bond that is correlated with the significant heme ruffing and saddling distortions, explains the unusually high O2 affinity of WT Tt H-NOX and the even higher affinity found in the P115A mutant.
Collapse
Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Weiqiao Zeng
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| | - Sandhya Muralidharan
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Elizabeth M Boon
- Department of Chemistry and the Institute of Chemical Biology and Drug Discovery, Stony Brook University , Stony Brook, New York 11794, United States
| | - Paul M Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University , Boston, Massachusetts 02115, United States
| |
Collapse
|
49
|
Liu Q, Zhou X, Liu H, Zhang X, Zhou Z. Fractional transfer of a free unpaired electron to overcome energy barriers in the formation of Fe(4+) from Fe(3+) during the core contraction of macrocycles: implication for heme distortion. Org Biomol Chem 2016; 13:2939-46. [PMID: 25609455 DOI: 10.1039/c4ob02429j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The free unpaired electron in Fe(3+) ions cannot be directly removed, and needs a transfer pathway with at least four steps to overcome the high energy barriers to form Fe(4+) ions. Fine changes in the electronic structure of Fe(3+) ions on spin conversion were identified through a deeper analysis of the diffraction, spectral and electrochemical data for six non-planar iron porphyrins. Fe(3+) ions can form four d electron tautomers as the compression of the central ion is increased. This indicates that the Fe(3+) ion undergoes a multistep electron transfer where the total energy gap of electron transfer is split into several smaller gaps to form high-valent Fe(4+) ions. We find that the interchange of these four electron tautomers is clearly related to the core size of the macrocycle in the current series. The large energy barrier to produce iron(iv) complexes is overcome through a gradient effect of multiple energy levels. In addition, a possible porphyrin Fe(3+)˙ radical may be formed from its stable isoelectronic form, porphyrin Fe(3+), under strong core contraction. These results indicate the important role of heme distortion in its catalytic oxidation functions.
Collapse
Affiliation(s)
- Qiuhua Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of 'Theoretical Organic Chemistry and Function Molecule' of the Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.
| | | | | | | | | |
Collapse
|
50
|
Graves AB, Graves MT, Liptak MD. Measurement of Heme Ruffling Changes in MhuD Using UV–vis Spectroscopy. J Phys Chem B 2016; 120:3844-53. [DOI: 10.1021/acs.jpcb.6b01497] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda B. Graves
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Max T. Graves
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Matthew D. Liptak
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| |
Collapse
|