1
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Olson JS. Kinetic mechanisms for O 2 binding to myoglobins and hemoglobins. Mol Aspects Med 2021; 84:101024. [PMID: 34544605 DOI: 10.1016/j.mam.2021.101024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 11/29/2022]
Abstract
Antonini and Brunori's 1971 book "Hemoglobin and Myoglobin in Their Reactions with Ligands" was a truly remarkable publication that summarized almost 100 years of research on O2 binding to these globins. Over the ensuing 50 years, ultra-fast laser photolysis techniques, high-resolution and time resolved X-ray crystallography, molecular dynamics simulations, and libraries of recombinant myoglobin (Mb) and hemoglobin (Hb) variants have provided structural interpretations of O2 binding to these proteins. The resultant mechanisms provide quantitative descriptions of the stereochemical factors that govern overall affinity, including proximal and distal steric restrictions that affect iron reactivity and favorable positive electrostatic interactions that preferentially stabilize bound O2. The pathway for O2 uptake and release by Mb and subunits of Hb has been mapped by screening libraries of site-directed mutants in laser photolysis experiments. O2 enters mammalian Mb and the α and β subunits of human HbA through a channel created by upward and outward rotation of the distal His at the E7 helical position, is non-covalently captured in the interior of the distal cavity, and then internally forms a bond with the heme Fe(II) atom. O2 dissociation is governed by disruption of hydrogen bonding interactions with His (E7), breakage of the Fe(II)-O2 bond, and then competition between rebinding and escape through the E7-gate. The structural features that govern the rates of both the individual steps and overall reactions have been determined and provide the framework for: (1) defining the physiological functions of specific globins and their evolution; (2) understanding the clinical features of hemoglobinopathies; and (3) designing safer and more efficient acellular hemoglobin-based oxygen carriers (HBOCs) for transfusion therapy, organ preservation, and other commercially relevant O2 transport and storage processes.
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Affiliation(s)
- John S Olson
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
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2
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Le Poul N, Colasson B, Thiabaud G, Dit Fouque DJ, Iacobucci C, Memboeuf A, Douziech B, Řezáč J, Prangé T, de la Lande A, Reinaud O, Le Mest Y. Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic. Chem Sci 2018; 9:8282-8290. [PMID: 30542577 PMCID: PMC6240898 DOI: 10.1039/c8sc03124j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/29/2018] [Indexed: 11/21/2022] Open
Abstract
Functionality of enzymes is strongly related to water dynamic processes.
Functionality of enzymes is strongly related to water dynamic processes. The control of the redox potential for metallo-enzymes is intimately linked to the mediation of water molecules in the first and second coordination spheres. Here, we report a unique example of supramolecular control of the redox properties of a biomimetic monocopper complex by water molecules. It is shown that the copper complex based on a calix[6]arene covalently capped with a tetradentate [tris(2-methylpyridyl)amine] (tmpa) core, embedding the metal ion in a hydrophobic cavity, can exist in three different states. The first system displays a totally irreversible redox behaviour. It corresponds to the reduction of the 5-coordinate mono-aqua-CuII complex, which is the thermodynamic species in the +II state. The second system is detected at a high redox potential. It is ascribed to an “empty cavity” or “water-free” state, where the CuI ion sits in a 4-coordinate trigonal environment provided by the tmpa cap. This complex is the thermodynamic species in the +I state under “dry conditions”. Surprisingly, a third redox system appears as the water concentration is increased. Under water-saturation conditions, it displays a pseudo-reversible behaviour at a low scan rate at the mid-point from the water-free and aqua species. This third system is not observed with the Cu-tmpa complex deprived of a cavity. In the calix[6]cavity environment, it is ascribed to a species where a pair of water molecules is hosted by the calixarene cavity. A molecular mechanism for the CuII/CuI redox process with an interplay of (H2O)x (x = 0, 1, 2) hosting is proposed on the basis of computational studies. Such an unusual behaviour is ascribed to the unexpected stabilization of the CuI state by inclusion of the pair of water molecules. This phenomenon strongly evidences the drastic influence of the interaction between water molecules and a hydrophobic cavity on controlling the thermodynamics and kinetics of the CuII/CuI electron transfer process.
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Affiliation(s)
- Nicolas Le Poul
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Benoit Colasson
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Grégory Thiabaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Dany Jeanne Dit Fouque
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Claudio Iacobucci
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Antony Memboeuf
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Bénédicte Douziech
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Flemingovonám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Thierry Prangé
- Laboratoire de Cristallographie et de Résonance Magnétique Nucléaire , Biologiques (CNRS UMR 8015) , Université Paris Descartes , 4, Avenue de l'Observatoire , 75006 Paris , France .
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , UMR CNRS 8000 , Université Paris Sud , 91405 Orsay , France .
| | - Olivia Reinaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Yves Le Mest
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
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Watanabe M, Kanai Y, Nakamura S, Nishimura R, Shibata T, Momotake A, Yanagisawa S, Ogura T, Matsuo T, Hirota S, Neya S, Suzuki A, Yamamoto Y. Synergistic Effect of Distal Polar Interactions in Myoglobin and Their Structural Consequences. Inorg Chem 2018; 57:14269-14279. [DOI: 10.1021/acs.inorgchem.8b02302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Life Science, University of Hyogo,
Sayo-cho, Sayo-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo,
Sayo-cho, Sayo-gun, Hyogo 678-1297, Japan
| | - Takashi Matsuo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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4
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Boubeta FM, Boechi L, Estrin D, Patrizi B, Di Donato M, Iagatti A, Giordano D, Verde C, Bruno S, Abbruzzetti S, Viappiani C. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125. J Phys Chem B 2018; 122:11649-11661. [PMID: 30230844 DOI: 10.1021/acs.jpcb.8b07682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites have been associated with cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins (a family of microbial heme-proteins of yet-unclear function) applying molecular dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue. The CO rebinding kinetics of the former highlight several geminate phases, with an unusually long-lived geminate intermediate. An articulated tunnel with at least two distinct docking sites was identified by analysis of molecular dynamics simulations and was suggested to be at the origin of the unusual geminate rebinding phase. Water molecules are present in the distal pocket, but their stabilization by TrpG8, TyrB10, and HisCD1 is much weaker than in thermophilic Thermobifida fusca truncated hemoglobin, resulting in a faster geminate rebinding. Our results support the hypothesis that weaker water-molecule interactions at the reaction site are associated with cold adaptation.
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Affiliation(s)
- Fernando M Boubeta
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Leonardo Boechi
- Instituto de Calculo, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , C1428EGA Buenos Aires , Argentina
| | - Dario Estrin
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Barbara Patrizi
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Mariangela Di Donato
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Alessandro Iagatti
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , Parco Area delle Scienze 23A , 43124 , Parma , Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
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5
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Abbruzzetti S, Allegri A, Bidon-Chanal A, Ogata H, Soavi G, Cerullo G, Bruno S, Montali C, Luque FJ, Viappiani C. Electrostatic Tuning of the Ligand Binding Mechanism by Glu27 in Nitrophorin 7. Sci Rep 2018; 8:10855. [PMID: 30022039 PMCID: PMC6052033 DOI: 10.1038/s41598-018-29182-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/02/2018] [Indexed: 12/29/2022] Open
Abstract
Nitrophorins (NP) 1-7 are NO-carrying heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus. The isoform NP7 displays peculiar properties, such as an abnormally high isoelectric point, the ability to bind negatively charged membranes, and a strong pH sensitivity of NO affinity. A unique trait of NP7 is the presence of Glu in position 27, which is occupied by Val in other NPs. Glu27 appears to be important for tuning the heme properties, but its influence on the pH-dependent NO release mechanism, which is assisted by a conformational change in the AB loop, remains unexplored. Here, in order to gain insight into the functional role of Glu27, we examine the effect of Glu27 → Val and Glu27 → Gln mutations on the ligand binding kinetics using CO as a model. The results reveal that annihilation of the negative charge of Glu27 upon mutation reduces the pH sensitivity of the ligand binding rate, a process that in turn depends on the ionization of Asp32. We propose that Glu27 exerts a through-space electrostatic action on Asp32, which shifts the pKa of the latter amino acid towards more acidic values thus reducing the pH sensitivity of the transition between open and closed states.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
| | - Alessandro Allegri
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy
| | - Axel Bidon-Chanal
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain
| | - Hideaki Ogata
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.,Institute of Low Temperature Science, Hokkaido University Kita19-Nishi8, Kita-ku, 060-0819, Sapporo, Japan
| | - Giancarlo Soavi
- Cambridge Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge, CB3 OFA, UK
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
| | - Chiara Montali
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain.
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
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6
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Gorski A, Starukhin A, Stavrov SS. Mössbauer spectroscopy as a probe of electric field in heme pocket of deoxyheme proteins: theoretical approach. J Radioanal Nucl Chem 2017. [DOI: 10.1007/s10967-017-5294-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Esquerra RM, Bibi BM, Tipgunlakant P, Birukou I, Soman J, Olson JS, Kliger DS, Goldbeck RA. Role of Heme Pocket Water in Allosteric Regulation of Ligand Reactivity in Human Hemoglobin. Biochemistry 2016; 55:4005-17. [PMID: 27355904 PMCID: PMC4978812 DOI: 10.1021/acs.biochem.6b00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water molecules can enter the heme pockets of unliganded myoglobins and hemoglobins, hydrogen bond with the distal histidine, and introduce steric barriers to ligand binding. The spectrokinetics of photodissociated CO complexes of human hemoglobin and its isolated α and β chains were analyzed for the effect of heme hydration on ligand rebinding. A strong coupling was observed between heme hydration and quaternary state. This coupling may contribute significantly to the 20-60-fold difference between the R- and T-state bimolecular CO binding rate constants and thus to the modulation of ligand reactivity that is the hallmark of hemoglobin allostery. Heme hydration proceeded over the course of several kinetic phases in the tetramer, including the R to T quaternary transition. An initial 150 ns hydration phase increased the R-state distal pocket water occupancy, nw(R), to a level similar to that of the isolated α (∼60%) and β (∼10%) chains, resulting in a modest barrier to ligand binding. A subsequent phase, concurrent with the first step of the R → T transition, further increased the level of heme hydration, increasing the barrier. The final phase, concurrent with the final step of the allosteric transition, brought the water occupancy of the T-state tetramer, nw(T), even higher and close to full occupancy in both the α and β subunits (∼90%). This hydration level could present an even larger barrier to ligand binding and contribute significantly to the lower iron reactivity of the T state toward CO.
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Affiliation(s)
- Raymond M. Esquerra
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Bushra M. Bibi
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Pooncharas Tipgunlakant
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Ivan Birukou
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - Jayashree Soman
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - John S. Olson
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - David S. Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Robert A. Goldbeck
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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8
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Bustamante JP, Abbruzzetti S, Marcelli A, Gauto D, Boechi L, Bonamore A, Boffi A, Bruno S, Feis A, Foggi P, Estrin DA, Viappiani C. Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins. J Phys Chem B 2014; 118:1234-45. [PMID: 24410478 DOI: 10.1021/jp410724z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
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9
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Cerda JF, Roeder MH, Houchins DN, Guzman CX, Amendola EJ, Castorino JD, Fritz AL. Electrochemical determination of heme-linked pKa values and the importance of using fluoride binding in heme proteins. Anal Biochem 2013; 443:75-7. [DOI: 10.1016/j.ab.2013.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 11/25/2022]
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10
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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Lapelosa M, Abrams CF. A computational study of water and CO migration sites and channels inside myoglobin. J Chem Theory Comput 2013; 9:1265-1271. [PMID: 23505344 DOI: 10.1021/ct300862j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pathways are computed for transport of H2O and CO in myoglobin (Mb), using the single sweep and zero-temperature string methods in a fully atomistic, explicitly solvated model system. Our predictions of sites and barriers in the pathways for CO transport agree with previous studies. For H2O, we predict a binding site in the distal pocket (DP), in agreement with crystallographic observations, and another one close to Leu 29 which explains the importance of this residue in controlling the pocket's hydrophobicity, as well as disordered minima in the largely apolar xenon cavities. In particular, H2O can occupy and transition among the xenon cavities, Xe4, Xe2, and Xe3. Our results support the hypothesis that the thermodynamically most favorable entry/exit portal for H2O is the so-called histidine gate (HG), the same as for CO. This result, along with the observation of water occupation of both DP and apolar Xe cavities, suggest that water and small gas molecules like CO compete for access to the protein interior, and therefore models of gas molecule transport within proteins should also explicitly consider water transport.
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Affiliation(s)
- Mauro Lapelosa
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, 19104 USA
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12
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Nasief NN, Tan H, Kong J, Hangauer D. Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes. J Med Chem 2012; 55:8283-302. [PMID: 22894131 DOI: 10.1021/jm300472k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.
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Affiliation(s)
- Nader N Nasief
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
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13
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Birukou I, Soman J, Olson JS. Blocking the gate to ligand entry in human hemoglobin. J Biol Chem 2010; 286:10515-29. [PMID: 21193395 DOI: 10.1074/jbc.m110.176271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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Esquerra RM, López-Peña I, Tipgunlakant P, Birukou I, Nguyen RL, Soman J, Olson JS, Kliger DS, Goldbeck RA. Kinetic spectroscopy of heme hydration and ligand binding in myoglobin and isolated hemoglobin chains: an optical window into heme pocket water dynamics. Phys Chem Chem Phys 2010; 12:10270-8. [PMID: 20668762 DOI: 10.1039/c003606b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The entry of a water molecule into the distal heme pocket of pentacoordinate heme proteins such as myoglobin and the alpha,beta chains of hemoglobin can be detected by time-resolved spectroscopy in the heme visible bands after photolysis of the CO complex. Reviewing the evidence from spectrokinetic studies of Mb variants, we find that this optical method measures the occupancy of non(heme)coordinated water in the distal pocket, n(w), with high fidelity. This evidence further suggests that perturbation of the kinetic barrier presented by distal pocket water is often the dominant mechanism by which active site mutations affect the bimolecular rate constant for CO binding. Water entry into the heme pockets of isolated hemoglobin subunits was detected by optical methods. Internal hydration is higher in the native alpha chains than in the beta chains, in agreement with previous crystallographic results for the subunits within Hb tetramers. The kinetic parameters obtained from modeling of the water entry and ligand rebinding in Mb mutants and native Hb chains are consistent with an inverse dependence of the bimolecular association rate constant on the water occupancy factor. This correlation suggests that water and ligand mutually exclude one another from the distal pockets of both types of hemoglobin chains and myoglobin.
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Affiliation(s)
- Raymond M Esquerra
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
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Jinendra B, Tamaki K, Kuroki S, Vassileva M, Yoshida S, Tsenkova R. Near infrared spectroscopy and aquaphotomics: Novel approach for rapid in vivo diagnosis of virus infected soybean. Biochem Biophys Res Commun 2010; 397:685-90. [PMID: 20570650 DOI: 10.1016/j.bbrc.2010.06.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/02/2010] [Indexed: 11/15/2022]
Abstract
Near infrared spectroscopy with aquaphotomics as a novel approach was assessed for the diagnosis of soybean plants (Glycine max) infected with soybean mosaic virus (SMV) at latent symptomless stage of the disease. Near infrared (NIR) leaf spectra (in the range of 730-1025nm) acquired from soybean plants with and without the inoculation of SMV were used. Leaf samples from all plants were assayed with enzyme-linked immunosorbent assay (ELISA) to confirm the infection. Previously reported NIR band for water at 970nm and two new bands at 910nm and 936nm in the water specific region of NIR were found to be markedly sensitive to the SMV infection 2weeks prior to the appearance of visual symptoms on infected leaves. The spectral calibration model soft independent modeling of class analogy (SIMCA), predicted the disease with 91.6% sensitivity and 95.8% specificity when the second order derivative of the individual plant averaged spectra were used. The study shows the potential of NIR spectroscopy with its novel approach to elucidate latent biochemical and biophysical information of an infection as it allowed successful discrimination of SMV infected plant from healthy at the early symptomless stage of the disease.
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Affiliation(s)
- Balasuriya Jinendra
- Department of Environmental Information and Bio Production Engineering, Kobe University, 1-1 Rokko-dai, cho, 657-8501, Japan.
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Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M. Heme Proteins: The Role of Solvent in the Dynamics of Gates and Portals. J Am Chem Soc 2010; 132:5156-63. [DOI: 10.1021/ja909822d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Chemical Sciences, University of Cagliari, Sardinian Laboratory for Computational Materials Science SLACS (IOM-CNR), and Department of Physics, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato, Italy
| | - Arturo Robertazzi
- Department of Chemical Sciences, University of Cagliari, Sardinian Laboratory for Computational Materials Science SLACS (IOM-CNR), and Department of Physics, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato, Italy
| | - Mariano Casu
- Department of Chemical Sciences, University of Cagliari, Sardinian Laboratory for Computational Materials Science SLACS (IOM-CNR), and Department of Physics, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato, Italy
| | - Paolo Ruggerone
- Department of Chemical Sciences, University of Cagliari, Sardinian Laboratory for Computational Materials Science SLACS (IOM-CNR), and Department of Physics, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato, Italy
| | - Matteo Ceccarelli
- Department of Chemical Sciences, University of Cagliari, Sardinian Laboratory for Computational Materials Science SLACS (IOM-CNR), and Department of Physics, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato, Italy
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Maragliano L, Cottone G, Ciccotti G, Vanden-Eijnden E. Mapping the Network of Pathways of CO Diffusion in Myoglobin. J Am Chem Soc 2009; 132:1010-7. [DOI: 10.1021/ja905671x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Maragliano
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, Department of Physical and Astronomical Sciences and CNISM, University of Palermo, Palermo, Italy, Physics Department and CNISM Unit of Rome 1, University of Rome “La Sapienza”, Rome, Italy, and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012
| | - Grazia Cottone
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, Department of Physical and Astronomical Sciences and CNISM, University of Palermo, Palermo, Italy, Physics Department and CNISM Unit of Rome 1, University of Rome “La Sapienza”, Rome, Italy, and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012
| | - Giovanni Ciccotti
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, Department of Physical and Astronomical Sciences and CNISM, University of Palermo, Palermo, Italy, Physics Department and CNISM Unit of Rome 1, University of Rome “La Sapienza”, Rome, Italy, and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012
| | - Eric Vanden-Eijnden
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, Department of Physical and Astronomical Sciences and CNISM, University of Palermo, Palermo, Italy, Physics Department and CNISM Unit of Rome 1, University of Rome “La Sapienza”, Rome, Italy, and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012
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