1
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Manz C, Kobitski AY, Samanta A, Nienhaus K, Jäschke A, Nienhaus GU. Exploring the energy landscape of a SAM-I riboswitch. J Biol Phys 2021; 47:371-386. [PMID: 34698957 PMCID: PMC8603990 DOI: 10.1007/s10867-021-09584-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022] Open
Abstract
SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg2+ and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg2+ concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription.
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Affiliation(s)
- Christoph Manz
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Andrei Yu Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.,Department of Chemistry, Uppsala University, Box 538, 751 21, Uppsala, Sweden
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany. .,Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green St, Urbana, IL, 61801, USA.
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2
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Ren HC, Ji LX, Chen TN, Yuan JN, Huang YY, Wei DQ, Ji GF, Zhang ZM. Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study. J Phys Chem B 2020; 124:9570-9578. [PMID: 33073576 DOI: 10.1021/acs.jpcb.0c06251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is no doubt that electric fields of a specific frequency and intensity could excite certain vibrational modes of a macromolecule, which alters its mode coupling and conformation. Motivated by recent experiments and theories, we study the mode coupling between the Fe-CO mode and CO-stretch mode and vibration energy transfer among the active site and proteins in carboxyhemoglobin (HbCO) under different electric fields using the quasi-static two-dimensional infrared spectra. This study uses iron-porphyrin-imidazole-CO and two distal histidines in HbCO as the subsystem. The potential energy and dipole moment surfaces of the subsystem are calculated using an all-electron ab initio (B3LYP-D3(BJ)) method with the basis set Lanl2dz for the Fe atom and 6-31G(d,p) for C, H, O, and N atoms. Although the subsystem is reduced dimensionally, the anharmonic frequency and anharmonicity of the CO-stretch mode show excellent agreement with experimental values. We use the revealing noncovalent interaction method to confirm the hydrogen bond between the Hε atom of the His63 and the CO molecule. Our study confirms that the mode coupling between the Fe-CO mode and CO-stretch mode does not exist when the subsystem is free of electric field perturbation, which is coupled when the electric field is -0.5142 V/nm. In addition, with the increases of distance between the active site and the His92, there is no vibrational energy transfer between them when the electric field is 1.028 V/nm. We believe that our work could provide new ideas for increasing the dissociation efficiency of the Fe-CO bond and theoretical references for experimental research.
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Affiliation(s)
- Hai Chao Ren
- School of Physical Sciences, University of Science and Technology of China, Hefei 230000, China.,National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621999, China
| | - Lin Xiang Ji
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Tu Nan Chen
- The First Affiliated Hospital, Army Medical University, Chongqing 400038, China
| | - Jiao Nan Yuan
- College of Science, Henan University of Technology, Zhengzhou 450001, China
| | - Yao Yao Huang
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621999, China
| | - Dong-Qing Wei
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China.,College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang Fu Ji
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics, Mianyang 621999, China
| | - Zeng Ming Zhang
- School of Physical Sciences, University of Science and Technology of China, Hefei 230000, China
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3
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Gallagher AT, Malliakas CD, Harris TD. CO Binding at a Four-Coordinate Cobaltous Porphyrin Site in a Metal–Organic Framework: Structural, EPR, and Gas Adsorption Analysis. Inorg Chem 2017; 56:4655-4662. [DOI: 10.1021/acs.inorgchem.7b00292] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Audrey T. Gallagher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Christos D. Malliakas
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - T. David Harris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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4
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Frauenfelder H. Ask not what physics can do for biology—ask what biology can do for physics. Phys Biol 2014; 11:053004. [DOI: 10.1088/1478-3975/11/5/053004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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5
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Zhang P, Ahn SW, Straub JE. “Strange Kinetics” in the Temperature Dependence of Methionine Ligand Rebinding Dynamics in Cytochrome c. J Phys Chem B 2013; 117:7190-202. [DOI: 10.1021/jp400481m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ping Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Steven Wooseok Ahn
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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6
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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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7
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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8
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Chillemi G, De Santis S, Falconi M, Mancini G, Migliorati V, Battistoni A, Pacello F, Desideri A, D'Angelo P. Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from Haemophilus ducreyi: in silico and in vitro evidences. J Biomol Struct Dyn 2012; 30:269-79. [PMID: 22686457 DOI: 10.1080/07391102.2012.680028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations have been jointly applied to the study of the Cu,Zn superoxide dismutase from Haemophilus ducreyi (HdSOD) in interaction with the carbon monoxide molecule. The configurational flexibility of the Fe(II)-heme group, intercalated between the two subunits, has been sampled by MD simulations and included in the XANES data analysis without optimization in the structural parameter space. Our results provide an interpretation of the observed discrepancy in the Fe-heme distances as detected by extended X-ray absorption fine structure (EXAFS) spectroscopy and the classical XANES analysis, in which the structural parameters are optimized in a unique structure. Moreover, binding of the CO molecule to the heme induces a long range effect on the Cu,Zn active site, as evidenced by both MD simulations and in vitro experiments. MD simulation of the CO bound system, in fact, highlighted a structural rearrangement of the protein-protein hydrogen bond network in the region of the Cu,Zn active site, correlated with an increase in water accessibility at short distance from the copper atom. In line, in vitro experiments evidenced an increase of copper accessibility to a chelating agent when the CO molecule binds to the heme group, as compared to a heme deprived HdSOD. Altogether, our results support the hypothesis that the HdSOD is a heme-sensor protein, in which binding to small gaseous molecules modulates the enzyme superoxide activity as an adaptive response to the bacterial environment.
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9
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Zhang P, Małolepsza E, Straub JE. Dynamics of Methionine Ligand Rebinding in Cytochrome c. J Phys Chem B 2012; 116:6980-90. [DOI: 10.1021/jp300783j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ping Zhang
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
| | - Edyta Małolepsza
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
| | - John E. Straub
- Department
of Chemistry, Boston University, Boston,
Massachusetts 02215, United States
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10
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Holzhacker C, Standfest-Hauser CM, Puchberger M, Mereiter K, Veiros LF, Calhorda MJ, Carvalho MD, Ferreira LP, Godinho M, Hartl F, Kirchner K. Reversible Addition of CO to Coordinatively Unsaturated High-Spin Iron(II) Complexes. Organometallics 2011. [DOI: 10.1021/om200711q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | - Luis F. Veiros
- Centro de Quı́mica Estrutural,
Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001 Lisboa, Portugal
| | | | | | - Liliana P. Ferreira
- Departamento Fı́sica,
Faculdade Ciências e Tecnologia, Universidade de Coimbra, 3004-516 Coimbra, Portugal
| | | | - František Hartl
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD,
United Kingdom
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11
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Kalay Z. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry. Crit Rev Biochem Mol Biol 2011; 46:310-26. [DOI: 10.3109/10409238.2011.582081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ziya Kalay
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
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12
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Benito-Garagorri D, Lagoja I, Veiros LF, Kirchner KA. Reactivity of coordinatively unsaturated iron complexes towards carbon monoxide: to bind or not to bind? Dalton Trans 2011; 40:4778-92. [PMID: 21380474 DOI: 10.1039/c0dt01636e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An overview of the reactivity of coordinatively unsaturated iron complexes (in most cases Fe(II)) towards carbon monoxide is presented. Unsaturated iron complexes are known with coordination numbers (CN) of two to five adopting linear or slightly bent (CN = 2), trigonal (CN = 3), tetrahedral, square planar or trigonal pyramidal (CN = 4), and square-pyramidal or trigonal-bipyramidal geometries (CN = 5), respectively. The binding of CO depends strongly on the number and the nature of co-ligands (overall ligand field strength), the charge of the complex, the complex geometry, and the spin state of the unsaturated metal center. In many cases, CO addition to high-spin iron complexes takes place with concomitant spin state changes forming compounds in the lowest possible spin state, i.e., with S = 0. In several other cases, however, the addition of CO is reversible or is even totally rejected altogether for either thermodynamic or kinetic reasons. In the case of the latter such reactions are termed "spin-blocked" or "spin forbidden".
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Affiliation(s)
- David Benito-Garagorri
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, A-1060, Vienna, Austria.
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13
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Gordon JC, Kubas GJ. Perspectives on How Nature Employs the Principles of Organometallic Chemistry in Dihydrogen Activation in Hydrogenases. Organometallics 2010. [DOI: 10.1021/om100436c] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John C. Gordon
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Gregory J. Kubas
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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14
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Nienhaus K, Dominici P, Astegno A, Abbruzzetti S, Viappiani C, Nienhaus GU. Ligand migration and binding in nonsymbiotic hemoglobins of Arabidopsis thaliana. Biochemistry 2010; 49:7448-58. [PMID: 20666470 DOI: 10.1021/bi100768g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We have studied carbon monoxide (CO) migration and binding in the nonsymbiotic hemoglobins AHb1 and AHb2 of Arabidopsis thaliana using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures. Both proteins have similar amino acid sequences but display pronounced differences in ligand binding properties, at both physiological and cryogenic temperatures. Near neutral pH, the distal HisE7 side chain is close to the heme-bound ligand in the majority of AHb1-CO molecules, as indicated by a low CO stretching frequency at 1921 cm(-1). In this fraction, two CO docking sites can be populated, the primary site B and the secondary site C. When the pH is lowered, a high-frequency stretching band at approximately 1964 cm(-1) grows at the expense of the low-frequency band, indicating that HisE7 protonates and, concomitantly, moves away from the bound ligand. Geminate rebinding barriers are markedly different for the two conformations, and docking site C is not accessible in the low-pH conformation. Rebinding of NO ligands was observed only from site B of AHb1, regardless of conformation. In AHb2, the HisE7 side chain is removed from the bound ligand; rebinding barriers are low, and CO molecules can populate only primary docking site B. These results are interpreted in terms of differences in the active site structures and physiological functions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
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15
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D’Angelo P, Della Longa S, Arcovito A, Anselmi M, Di Nola A, Chillemi G. Dynamic Investigation of Protein Metal Active Sites: Interplay of XANES and Molecular Dynamics Simulations. J Am Chem Soc 2010; 132:14901-9. [DOI: 10.1021/ja1056533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paola D’Angelo
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Stefano Della Longa
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Alessandro Arcovito
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Massimiliano Anselmi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Alfredo Di Nola
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Giovanni Chillemi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
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16
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Walker VEJ, Castillo N, Matta CF, Boyd RJ. The Effect of Multiplicity on the Size of Iron(II) and the Structure of Iron(II) Porphyrins. J Phys Chem A 2010; 114:10315-9. [DOI: 10.1021/jp105842k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Victoria E. J. Walker
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4, and Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada, B3M 2J6
| | - Norberto Castillo
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4, and Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada, B3M 2J6
| | - Chérif F. Matta
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4, and Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada, B3M 2J6
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4J3, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada, T2N 1N4, and Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada, B3M 2J6
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17
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Nienhaus K, Nienhaus GU. Ligand dynamics in heme proteins observed by Fourier transform infrared-temperature derivative spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1030-41. [PMID: 20656073 DOI: 10.1016/j.bbapap.2010.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the investigation of protein-ligand interactions in heme proteins. Nitric oxide and carbon monoxide are attractive physiologically relevant ligands because their bond stretching vibrations give rise to strong mid-infrared absorption bands that can be measured with exquisite sensitivity and precision using photolysis difference spectroscopy at cryogenic temperatures. These stretching bands are fine-tuned by electrostatic interactions with the environment and, therefore, ligands can be utilized as local probes of structure and dynamics. Bound to the heme iron, the ligand stretching bands are susceptible to changes in the iron-ligand bond and the electric field at the active site. Upon photolysis, the vibrational bands display changes due to ligand relocation to docking sites within the protein, rotational motions of the ligand in these sites and protein conformational changes. Photolysis difference spectra taken over a wide temperature range (3-300K) using specific temperature protocols for sample photodissociation can provide detailed insights into both protein and ligand dynamics. Moreover, temperature-derivative spectroscopy (TDS) has proven to be a particularly powerful technique to study protein-ligand interactions. The FTIR-TDS technique has been extensively applied to studies of carbon monoxide binding to heme proteins, whereas measurements with nitric oxide are still scarce. Here we describe infrared cryo-spectroscopy and present a variety of applications to the study of protein-ligand interactions in heme proteins. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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18
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Benito-Garagorri D, Alves LG, Veiros LF, Standfest-Hauser CM, Tanaka S, Mereiter K, Kirchner K. Kinetically Controlled Formation of Octahedral trans-Dicarbonyl Iron(II) PNP Pincer Complexes: The Decisive Role of Spin-State Changes. Organometallics 2010. [DOI: 10.1021/om1001638] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Luis F. Veiros
- Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa, Portugal
| | | | | | - Kurt Mereiter
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9, A-1060 Vienna, Austria
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19
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Zhang F, Ai YJ, Luo Y, Fang WH. Nonadiabatic Histidine Dissociation of Hexacoordinate Heme in Neuroglobin Protein. J Phys Chem A 2010; 114:1980-4. [DOI: 10.1021/jp909887d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Feng Zhang
- Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yue-Jie Ai
- Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yi Luo
- Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing 100875, China
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20
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21
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Degtyarenko I, Biarnés X, Nieminen RM, Rovira C. Density-functional molecular dynamics studies of biologically relevant iron and cobalt complexes with macrocyclic ligands. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Kubas GJ. Fundamentals of H2 Binding and Reactivity on Transition Metals Underlying Hydrogenase Function and H2 Production and Storage. Chem Rev 2007; 107:4152-205. [DOI: 10.1021/cr050197j] [Citation(s) in RCA: 796] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Gregory J. Kubas
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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23
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Kondrashov DA, Montfort WR. Nonequilibrium dynamics simulations of nitric oxide release: comparative study of nitrophorin and myoglobin. J Phys Chem B 2007; 111:9244-52. [PMID: 17622170 DOI: 10.1021/jp071136n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrophorin 4 (NP4) is a heme protein that reversibly binds nitric oxide (NO), with release rates modulated by pH change. High-resolution structures of NP4 revealed that pH changes and NO binding induce a large conformational rearrangement in two loops that serve to protect the heme-bound NO molecule from solvent. We used extended (110 ns) molecular dynamics simulations of NP4 at pH 5 and pH 7, modeled by selective deprotonation of acidic groups. Conformational and dynamic changes were observed, consistent with those found in the crystal. Further, major solvent movement and NO escape were observed at pH 7, while the ligand remained in the heme binding pocket at pH 5. As a control, we also performed molecular dynamics (MD) simulations of sperm whale myoglobin, where NO migration into the interior cavities of the protein was observed, consistent with previous reports. We constructed a kinetic model of ligand escape to quantitatively relate the microscopic rate constants to the observed rates, and tested the predictions against the experimental data. The results suggest that release rates of diatomic molecules from heme proteins can be varied by several orders of magnitude through modest adjustments in geminate rebinding and gating behavior.
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Affiliation(s)
- Dmitry A Kondrashov
- Graduate Program in Applied Mathematics and Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA.
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24
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Sottini S, Abbruzzetti S, Viappiani C, Ronda L, Mozzarelli A. Determination of microscopic rate constants for CO binding and migration in myoglobin encapsulated in silica gels. J Phys Chem B 2007; 109:19523-8. [PMID: 16853522 DOI: 10.1021/jp054098l] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CO rebinding kinetics after nanosecond photolysis of myoglobin encapsulated in wet silica gels exhibits an enhanced geminate phase that allows the determination of the microscopic rate constants and the activation barriers for distinct ligand docking sites inside the protein matrix. Using a maximum entropy method, we demonstrate that the geminate phase can be well-described by a biphasic lifetime distribution, reflecting rebinding from the distal and proximal sites. Microscopic rates and activation barriers were estimated using a four-state model.
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Affiliation(s)
- Silvia Sottini
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43100 Parma, Italy
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25
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Amadei A, D’Abramo M, Daidone I, D’Alessandro M, Nola AD, Aschi M. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0197-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Strickland N, Harvey JN. Spin-Forbidden Ligand Binding to the Ferrous−Heme Group: Ab Initio and DFT Studies. J Phys Chem B 2007; 111:841-52. [PMID: 17249828 DOI: 10.1021/jp064091j] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential energy surfaces (PESs) and associated energy barriers that characterize the spin-forbidden recombination reactions of the gas-phase ferrous deoxy-heme group with CO, NO, and H2O ligands have been calculated using density functional theory (DFT). The bond energy for binding of O2 has also been calculated. Extensive large basis set CCSD(T) calculations on two small models of the heme group have been used to calibrate the accuracy of different DFT functionals for treating these systems. Pure functionals are shown to overestimate the stability of the low-spin forms of the deoxy-heme model, and to overestimate the binding energy of H2O and CO, whereas hybrid functionals such as B3PW91 and B3LYP yield accurate results. Accordingly, the latter functionals have been used to explore the PESs for binding. CO binding is found to involve a significant barrier of ca. 3 kcal mol-1 due to the need to change from the deoxy-heme quintet ground state to the bound singlet state. Binding of water does not involve a barrier, but the resulting bond is weak and may be further weakened in the protein environment, which should explain why water binding is not usually observed in heme proteins such as myoglobin. NO binding involves a low barrier, which is consistent with observed rapid geminate recombination. The calculated bond energies are in good agreement with previous reported values and in fair agreement with experiment for CO and O2. The value for NO is significantly lower than the experimentally derived bond energy, suggesting that B3LYP is less accurate in this case.
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Affiliation(s)
- Nikki Strickland
- Centre for Computational Chemistry and School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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27
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Abbruzzetti S, Bruno S, Faggiano S, Grandi E, Mozzarelli A, Viappiani C. Time-resolved methods in Biophysics. 2. Monitoring haem proteins at work with nanosecond laser flash photolysis. Photochem Photobiol Sci 2006; 5:1109-20. [PMID: 17136275 DOI: 10.1039/b610236k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Haem proteins have long been the most studied proteins in biophysics, and have become paradigms for the characterization of fundamental biomolecular processes as ligand binding and regulatory conformational transitions. The presence of the haem prosthetic group, the absorbance spectrum of which has a ligation sensitive region conveniently located in the UV-visible range, has offered a powerful and sensitive tool for the investigation of molecular functions. The central Fe atom is capable of reversibly binding diatomic ligands, including O(2), CO, and NO. The Fe-ligand bond is photolabile, and a reactive unligated state can be transiently generated with a pulsed laser. The photodissociated ligands quickly rebind to the haem and the process can be monitored by transient absorbance methods. The ligand rebinding kinetics reflects protein dynamics and ligand migration within the protein inner cavities. The characterization of these processes was done in the past mainly by low temperature experiments. The use of silica gels to trap proteins allows the characterization of internal ligand dynamics at room temperature. In order to show the potential of the laser flash photolysis techniques, combined with modern numerical analysis methods, we report experiments conducted on two non-symbiotic haemoglobins from Arabidopsis thaliana. The comparison between time courses recorded on haemoglobins in solution and encapsulated in silica gels allows for the highlighting of different interplays between protein dynamics and ligand migration.
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28
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Hardman NJ, Fang X, Scott BL, Wright RJ, Martin RL, Kubas GJ. High-spin diimine complexes of iron(II) reject binding of carbon monoxide: theoretical analysis of thermodynamic factors inhibiting or favoring spin-crossover. Inorg Chem 2006; 44:8306-16. [PMID: 16270969 DOI: 10.1021/ic050966h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new series of Fe(II) complexes, FeCl2[N(R)=C(Me)C(Me)=N(R)], containing diimine ligands with hemilabile sidearms R (R = CH2(CH2)2NMe2, 1, CH2(CH2)2OMe, 2, CH2(CH2)2SMe), 3) were synthesized. The crystal structure of 1 showed 6-coordination where both amine arms were attached, whereas 2 was a 5-coordinate 16e species with one methoxy arm dangling free. Extensive attempts were made to bind CO to these species to synthesize precursors for dihydrogen complexes but were unsuccessful. Reaction of 1 with 1 or 2 equiv of AgOTf under CO atmosphere resulted in isolation of only a 6-coordinate bis(triflate)-containing product [Fe[N(R)=C(Me)C(Me)=N(R)](OTf)2] (R = CH2(CH2)2NMe2), 5. Reaction of 5-coordinate 2 with AgSbF6 under CO did not give a CO adduct but afforded instead a dicationic dinuclear complex [Fe[N(R)=C(Me)C(Me)=N(R)](mu-Cl)]2[SbF6]2 (R = CH2(CH2)2OMe), 4, containing a weakly bound SbF6. Thus coordination of hard-donor anions to iron was favored over CO binding. The unexpected rejection of binding of CO is rationalized by the iron being in a high-spin state in this system and energetically incapable of spin crossover to a low-spin state. Theoretical calculations on CO interaction with Fe(II) centers in spin states S = 0, 1, and 2 for both the 16e complexes and their CO adducts aid further understanding of this problem. They show that interaction of CO with a high-spin 5-coordinate Fe model diimine complex is essentially thermoneutral but is exergonic by about 48 kcal/mol to a comparable but low-spin diphosphine fragment. Spin crossover is thus disfavored thermodynamically rather than kinetically (e.g. a "spin block" effect); i.e., the ligand field strengths of the primarily N-donor groups are apparently insufficient to give a low-spin CO adduct.
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Affiliation(s)
- Ned J Hardman
- Chemistry Division and Theoretical Division, Los Alamos National Laboratory, MS-J514, Los Alamos, New Mexico 87545, USA
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29
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Danielsson J, Banushkina P, Nutt DR, Meuwly M. Computer simulations of structures, energetics and dynamics of myoglobin ··· ligand complexes. INT REV PHYS CHEM 2006. [DOI: 10.1080/01442350600798253] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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Fernandez-Alberti S, Bacelo DE, Binning RC, Echave J, Chergui M, Lopez-Garriga J. Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility. Biophys J 2006; 91:1698-709. [PMID: 16782787 PMCID: PMC1544295 DOI: 10.1529/biophysj.106.081646] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamics of Hemoglobin I (HbI) from the clam Lucina pectinata, from wild-type sperm whale (SW) myoglobin, and from the L29F/H64Q/V68F triple mutant of SW, both unligated and bound to hydrogen sulfide (H2S), have been studied in molecular dynamics simulations. Features that account for differences in H2S affinity among the three have been examined. Our results verify the existence of an unusual heme rocking motion in unligated HbI that can promote the entrance of large ligands such as H2S. The FQF-mutant partially reproduces the amplitude and relative orientation of the motion of HbI's heme group. Therefore, besides introducing favorable electrostatic interactions with H2S, the three mutations in the distal pocket change the dynamic properties of the heme group. The active-site residues Gln-64(E7), Phe-43(CD1), and His-93(F8) are also shown to be more flexible in unligated HbI than in FQF-mutant and SW. Further contributions to H2S affinity come from differences in hydrogen bonding between the heme propionate groups and nearby amino acid residues.
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31
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Guallar V, Jarzecki AA, Friesner RA, Spiro TG. Modeling of Ligation-Induced Helix/Loop Displacements in Myoglobin: Toward an Understanding of Hemoglobin Allostery. J Am Chem Soc 2006; 128:5427-35. [PMID: 16620114 DOI: 10.1021/ja057318h] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combining quantum and molecular mechanics (QM/MM) methods and protein structure prediction algorithms, helix and loop movements are computed along the pathway of CO dissociation from myoglobin (Mb). The results are compared with high-resolution crystallographic data using sequence-displacement graphs. These graphs provide an unbiased method for evaluating main-chain segmental motions; they resolve an apparent disagreement between two sets of high-resolution crystal structures for MbCO and deoxyMb. The QM/MM modeling of the CO deligation reproduces the experimentally observed spin states and photodissociated crystal structure. The principal effect of CO dissociation is shown to be a concerted rotation of the E and F helices, which hold the heme like a clamshell. The rotation is a response to deligation forces, which impel the F helix away from the heme because of the Fe spin conversion, and which allow the E helix to collapse toward the heme as nonbonded contacts on the distal side are relieved. Additional helix and loop displacements stem from these primary events. In particular, the CD loop is found to be repositioned as a result of steric interactions with the water molecule that becomes H-bonded to the distal histidine in deoxyMb. A similar EF rotation and CD loop displacement are proposed to be the first steps along the allosteric pathway from the R to the T state in hemoglobin.
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Affiliation(s)
- Victor Guallar
- Department of Biochemistry, Washington University School of Medicine, St, Louis, Missouri 63108, USA
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32
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Zierkiewicz W, Privalov T. A computational study of oxidation of ruthenium porphyrins via ORuIV and ORuVIO species. Dalton Trans 2006:1867-74. [PMID: 16585974 DOI: 10.1039/b513482j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unrestricted density functional theory (UDFT) was applied to study the oxidation of ruthenium porphyrins, [RuP], via an interaction with molecular oxygen. The important role of dimeric [RuP] complexes, i.e. [RuP]-O2-[RuP], in the oxidation mechanism and particular in the cleavage of O-O bond of molecular oxygen has been studied. Geometries and relative Gibbs free energies of the intermediate Ru-complexes, i.e. dimeric oxo-Ru-porphyrins and O2Ru(II)-(or O2- Ru(III))-, ORu(IV)- and ORu(VI)O-porphyrins, were evaluated along the proposed reaction pathway. The detailed thermodynamic data of the oxidation reaction [Ru(II)P] --> O[Ru(IV)P] --> O[Ru(VI)P]O and important aspects of the vibrational spectra of an oxo-[RuP] has been presented.
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Affiliation(s)
- Wiktor Zierkiewicz
- Organic Chemistry, School of Chemistry and Engineering, Royal Institute of Technology (KTH), S-10044, Stockholm, Sweden
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33
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Khoroshun DV, Musaev DG, Morokuma K. Electronic reorganization: Origin of sigma trans promotion effect. J Comput Chem 2006; 28:423-41. [PMID: 17143866 DOI: 10.1002/jcc.20551] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Binding of two ligands trans to each other by some transition metal complexes may be cooperative [Khoroshun et al., Mol Phys 2002, 100, 523]. Several interesting consequent effects include (i) inverse relationship between bond strength and binding affinity; (ii) smaller coordination barriers to formation of weaker bonds; (iii) enhancement of Lewis acidity with increased number of ligands. We describe a simple model, sigma trans promotion effect (TPE), which considers electronic reorganization between two Lewis structures, and predicts the above-mentioned effects. The applied result of present study is the unified perspective on several facts of heme chemistry. Particularly, we reiterate an important but often overlooked notion, developed previously within the spin pairing model [Drago and Corden, Acc Chem Res 1980, 13, 353], that, in hemoproteins, the proximal histidine and the distal ligand such as O2 or CO cooperate in promoting electronic reorganization. As a result, depopulation of dz2 orbital upon ligand binding contributes to the phenomenon of hemoglobin cooperativity. The presented density functional (B3LYP) calculations on realistic models, the processes of carbon monoxide binding by Fe(II) porphyrins and dinitrogen binding by triamido/triamidoamine Mo(III) complexes, particularly the evaluation of the coordination barriers due to spin-state change by location of the minima on seams of crossing, support the TPE model predictions. From a broader theoretical perspective, the present study would hopefully stimulate the development of much needed frameworks and tools for facile comparisons of wave functions and their properties between different geometries, species, and electronic states. Advancement of practical wave function comparisons may yield fresh qualitative perspectives on chemical reactivity, and promote better understanding of related concepts such as electronic reorganization.
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Affiliation(s)
- Dmitry V Khoroshun
- Cherry L. Emerson Center for Scientific Computation, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
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34
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Nutt DR, Meuwly M. Studying reactive processes with classical dynamics: rebinding dynamics in MbNO. Biophys J 2005; 90:1191-201. [PMID: 16326913 PMCID: PMC1367270 DOI: 10.1529/biophysj.105.071522] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mus of total simulation time) for the rebinding of NO to myoglobin. The unbound surface (Fe...NO) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.
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Affiliation(s)
- David R Nutt
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
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35
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Henkelman G, LaBute MX, Tung CS, Fenimore PW, McMahon BH. Conformational dependence of a protein kinase phosphate transfer reaction. Proc Natl Acad Sci U S A 2005; 102:15347-51. [PMID: 16227439 PMCID: PMC1255735 DOI: 10.1073/pnas.0506425102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. With the protein in TC, the motions involved in reaction are small, with only P(gamma) and the catalytic proton moving >0.5 A. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site.
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Affiliation(s)
- Graeme Henkelman
- Department of Chemistry and Biochemistry, University of Texas, 1 University Station A5300, Austin, TX 78712-0165, USA
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36
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Ye X, Yu A, Georgiev GY, Gruia F, Ionascu D, Cao W, Sage JT, Champion PM. CO rebinding to protoheme: investigations of the proximal and distal contributions to the geminate rebinding barrier. J Am Chem Soc 2005; 127:5854-61. [PMID: 15839683 PMCID: PMC2768272 DOI: 10.1021/ja042365f] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imidazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imidazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, H(p), to be 11 +/- 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: DeltaG(D) approximately 12 +/- 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin ( approximately 3 kJ/mol), then lead to a distal pocket enthalpic barrier of H(D) approximately 9 +/- 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements of the enthalpic MbCO rebinding barrier (18 +/- 2 kJ/mol).
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37
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Cordone L, Cottone G, Giuffrida S, Palazzo G, Venturoli G, Viappiani C. Internal dynamics and protein–matrix coupling in trehalose-coated proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:252-81. [PMID: 15886079 DOI: 10.1016/j.bbapap.2005.03.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Revised: 03/04/2005] [Accepted: 03/04/2005] [Indexed: 11/23/2022]
Abstract
We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water-trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q(B) containing or Q(B) deprived reaction centre from R. sphaeroides. Experimental results, together with the outcome of molecular dynamics simulations, concurred to give a picture of how water-containing matrices control the internal dynamics of the embedded proteins. This occurs, in particular, via the formation of hydrogen bond networks that anchor the protein surface to the surrounding matrix, whose stiffness increases by lowering the sample water content. In the conclusion section, we also briefly speculate on how the protein-matrix interactions observed in our samples may shed light on the protein-solvent coupling also in liquid aqueous solutions.
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Affiliation(s)
- Lorenzo Cordone
- Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo, Italy.
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38
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Nienhaus K, Olson JS, Franzen S, Nienhaus GU. The origin of stark splitting in the initial photoproduct state of MbCO. J Am Chem Soc 2005; 127:40-1. [PMID: 15631438 DOI: 10.1021/ja0466917] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ligand migration and binding in heme proteins have been measured by X-ray diffraction and time-resolved spectroscopy of photoproduct intermediates. In myoglobin (Mb), internal cavities serve as docking sites for carbon monoxide (CO) ligands. In these sites, the CO ligands display characteristic infrared (IR) stretching bands due to interactions with the local electrical field. In the primary docking site, a CO can reside in two opposite orientations, characterized by a doublet of infrared bands, B1 at approximately 2130 and B2 at approximately 2120 cm-1. To assign these bands to the specific orientations, we have reexamined the effects of mutating His64 and Val68 on the infrared stretching bands associated with the B1 and B2 photoproduct states. Wild-type, H64L, V68F, and H64L-V68F MbCO were selected for experimental and theoretical analyses. Fourier transform infrared (FTIR) spectroscopy and density functional theory (DFT) calculations were used to interpret the effects of the electrostatic environment on the B state bands. The imidazole side chain of His64 appears to be the primary cause of the observed Stark splitting. The high-frequency B1 band is assigned to the CO orientation in which the carbon (white atom) is directed toward the heme iron and the Nepsilon-H proton of His64. At low temperatures, CO molecules in the opposite orientational conformer, B2 with the O atom (red) toward His64, first rotate by 180 degrees into the more stable B1 state and then rebind.
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Affiliation(s)
- Karin Nienhaus
- University of Ulm, Department of Biophysics, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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39
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Kim S, Jin G, Lim M. Dynamics of Geminate Recombination of NO with Myoglobin in Aqueous Solution Probed by Femtosecond Mid-IR Spectroscopy. J Phys Chem B 2004. [DOI: 10.1021/jp0489020] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seongheun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Geunyeong Jin
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 609-735, Korea
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40
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Fenimore PW, Frauenfelder H, McMahon BH, Young RD. Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions. Proc Natl Acad Sci U S A 2004; 101:14408-13. [PMID: 15448207 PMCID: PMC521939 DOI: 10.1073/pnas.0405573101] [Citation(s) in RCA: 405] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mossbauer and neutron-scattering experiments, that fluctuations in the hydration shell control fast fluctuations in the protein. We call the first type solvent-slaved or alpha-fluctuations and the second type hydration-shell-coupled or beta-fluctuations. Solvent-slaved motions are similar to the alpha-fluctuations in glasses. Their temperature dependence can be approximated by a Vogel-Tammann-Fulcher relation and they are absent in a solid environment. Hydration-shell-coupled fluctuations are similar to the beta-relaxation in glasses. They can be approximated by a Ferry or an Arrhenius relation, are much reduced or absent in dehydrated proteins, and occur in hydrated proteins even if embedded in a solid. They can be responsible for internal processes such as the migration of ligands within myoglobin. The existence of two functionally important fluctuations in proteins, one slaved to bulk motions and the other coupled to hydration-shell fluctuations, implies that the environment can control protein functions through different avenues and that no real protein transition occurs at approximately 200 K. The large number of conformational substates is essential; proteins cannot function without this reservoir of entropy, which resides mainly in the hydration shell.
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Affiliation(s)
- P W Fenimore
- Theory Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Lim M, Jackson TA, Anfinrud PA. Orientational distribution of CO before and after photolysis of MbCO and HbCO: a determination using time-resolved polarized Mid-IR spectroscopy. J Am Chem Soc 2004; 126:7946-57. [PMID: 15212544 DOI: 10.1021/ja035475f] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The technique of time-resolved polarized mid-IR spectroscopy was used to probe the orientational distribution of carbon monoxide (CO) bound to and docked within horse myoglobin, sperm whale myoglobin, and human hemoglobin A in neutral pH solution at 283 K. An accurate determination of the orientation required that the experimentally measured polarization anisotropy be corrected for the effects of fractional photolysis in an optically thick sample. The experimental method measures the direction of the transition dipole, which is parallel to the CO bond axis when docked and nearly parallel when bound to the heme. The polarization anisotropy of bound CO is virtually the same for all protein systems investigated and is unchanging across its inhomogeneously broadened mid-IR absorption spectrum. From these results, it was concluded that the transition dipole moment of bound CO is oriented </=7 degrees from the heme plane normal. The polarized absorbance spectra of docked CO are similar for all protein systems investigated, but in stark contrast to bound CO, the polarization anisotropy is strongly correlated with vibrational frequency. The frequency-dependent anisotropy imposes severe constraints on the orientational probability distribution function of the transition dipole, which is well described as a dipole bathed in a Stark field whose out-of-plane motion is constrained by a simple double-well potential. The orientational and spatial constraints imposed on docked CO by the surrounding highly conserved amino acids serve to mediate ligand transport to and from the binding site and thereby control the rates and pathways for geminate ligand rebinding and ligand escape.
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Affiliation(s)
- Manho Lim
- Department of Chemistry, Pusan National University, Busan, 609-735, Korea
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Cao W, Ye X, Sjodin T, Christian JF, Demidov AA, Berezhna S, Wang W, Barrick D, Sage JT, Champion PM. Investigations of Photolysis and Rebinding Kinetics in Myoglobin Using Proximal Ligand Replacements. Biochemistry 2004; 43:11109-17. [PMID: 15323570 DOI: 10.1021/bi049077g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound H93G myoglobin (Mb) mutants to study the influence of the proximal ligand on the CO rebinding kinetics. In H93G mutants, where the proximal linkage with the protein is eliminated and the heme can bind exogenous ligands (e.g., imidazole, 4-bromoimidazole, pyridine, or dibromopyridine), we observe significant effects on the CO rebinding kinetics in the 10 ns to 10 ms time window. Resonance Raman spectra of the various H93G Mb complexes are also presented to aid in the interpretation of the kinetic results. For CO-bound H93G(dibromopyridine), we observe a rapid large-amplitude geminate phase with a fundamental CO rebinding rate that is approximately 45 times faster than for wild-type MbCO at 293 K. The absence of an iron proximal ligand vibrational mode in the 10 ns photoproduct Raman spectrum of CO-bound H93G(dibromopyridine) supports the hypothesis that proximal ligation has a significant influence on the kinetics of diatomic ligand binding to the heme.
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Affiliation(s)
- Wenxiang Cao
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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43
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Nutt DR, Meuwly M. Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin. Biophys J 2004; 85:3612-23. [PMID: 14645054 PMCID: PMC1303666 DOI: 10.1016/s0006-3495(03)74779-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3-7 cm(-1) (compared to the experimental value of 10 cm(-1)) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe...CO and Fe...OC) is 0.3 kcal mol(-1) and agrees well with the experimentally estimated value of 0.29 kcal mol(-1). A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.
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Affiliation(s)
- David R Nutt
- Department of Chemistry, University of Basel, CH-4056 Basel, Switzerland
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Cao W, Ye X, Georgiev GY, Berezhna S, Sjodin T, Demidov AA, Wang W, Sage JT, Champion PM. Proximal and Distal Influences on Ligand Binding Kinetics in Microperoxidase and Heme Model Compounds†. Biochemistry 2004; 43:7017-27. [PMID: 15170339 DOI: 10.1021/bi0497291] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound heme complexes to study proximal and distal influences on ligand rebinding kinetics. We report kinetics of CO rebinding to microperoxidase (MP) and 2-methylimidazole ligated Fe protoporphyrin IX in the 10 ns to 10 ms time window. We also report CO rebinding kinetics of MP in the 150 fs to 140 ps time window. For dilute, micelle-encapsulated (monodisperse) samples of MP, we do not observe the large amplitude geminate decay at approximately 100 ps previously reported in time-resolved IR measurements on highly concentrated samples [Lim, M., Jackson, T. A., and Anfinrud, P. A. (1997) J. Biol. Inorg. Chem. 2, 531-536]. However, for high concentration aggregated samples, we do observe the large amplitude picosecond CO geminate rebinding and find that it is correlated with the absence of the iron-histidine vibrational mode in the time-resolved Raman spectrum. On the basis of these results, the energetic significance of a putative distal pocket CO docking site proposed by Lim et al. may need to be reconsidered. Finally, when high concentration samples of native myoglobin (Mb) were studied as a control, an analogous increase in the geminate rebinding kinetics was not observed. This verifies that studies of Mb under dilute conditions are applicable to the more concentrated regime found in the cellular milieu.
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Affiliation(s)
- Wenxiang Cao
- Department of Physics and Center for Interdisciplinary Research on Complex System, Northeastern University, Boston, Massachusetts 02115, USA
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Sottini S, Viappiani C, Ronda L, Bettati S, Mozzarelli A. CO Rebinding Kinetics to Myoglobin- and R-State-Hemoglobin-Doped Silica Gels in the Presence of Glycerol. J Phys Chem B 2004. [DOI: 10.1021/jp049472g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silvia Sottini
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy; Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43100 Parma, Italy; Dipartimento di Sanità Pubblica, Università degli Studi di Parma, via Volturno 39, 43100 Parma, Italy; and Istituto Nazionale per la Fisica della Materia (INFM), c/o Dipartimento di Fisica, Università di Parma, parco area delle scienze 7A, 43100 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy; Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43100 Parma, Italy; Dipartimento di Sanità Pubblica, Università degli Studi di Parma, via Volturno 39, 43100 Parma, Italy; and Istituto Nazionale per la Fisica della Materia (INFM), c/o Dipartimento di Fisica, Università di Parma, parco area delle scienze 7A, 43100 Parma, Italy
| | - Luca Ronda
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy; Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43100 Parma, Italy; Dipartimento di Sanità Pubblica, Università degli Studi di Parma, via Volturno 39, 43100 Parma, Italy; and Istituto Nazionale per la Fisica della Materia (INFM), c/o Dipartimento di Fisica, Università di Parma, parco area delle scienze 7A, 43100 Parma, Italy
| | - Stefano Bettati
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy; Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43100 Parma, Italy; Dipartimento di Sanità Pubblica, Università degli Studi di Parma, via Volturno 39, 43100 Parma, Italy; and Istituto Nazionale per la Fisica della Materia (INFM), c/o Dipartimento di Fisica, Università di Parma, parco area delle scienze 7A, 43100 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy; Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43100 Parma, Italy; Dipartimento di Sanità Pubblica, Università degli Studi di Parma, via Volturno 39, 43100 Parma, Italy; and Istituto Nazionale per la Fisica della Materia (INFM), c/o Dipartimento di Fisica, Università di Parma, parco area delle scienze 7A, 43100 Parma, Italy
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Ugalde JM, Dunietz B, Dreuw A, Head-Gordon M, Boyd RJ. The Spin Dependence of the Spatial Size of Fe(II) and of the Structure of Fe(II)-Porphyrins. J Phys Chem A 2004. [DOI: 10.1021/jp0489119] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jesus M. Ugalde
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, PK 1072, 20018 Donostia, Euskadi (Spain), Department of Chemistry, University of California, Berkeley and Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Department of Chemistry, Dalhousie University, Halifax, N.S., B3H 4J3 Canada
| | - Barry Dunietz
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, PK 1072, 20018 Donostia, Euskadi (Spain), Department of Chemistry, University of California, Berkeley and Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Department of Chemistry, Dalhousie University, Halifax, N.S., B3H 4J3 Canada
| | - Andreas Dreuw
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, PK 1072, 20018 Donostia, Euskadi (Spain), Department of Chemistry, University of California, Berkeley and Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Department of Chemistry, Dalhousie University, Halifax, N.S., B3H 4J3 Canada
| | - Martin Head-Gordon
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, PK 1072, 20018 Donostia, Euskadi (Spain), Department of Chemistry, University of California, Berkeley and Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Department of Chemistry, Dalhousie University, Halifax, N.S., B3H 4J3 Canada
| | - Russell J. Boyd
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, PK 1072, 20018 Donostia, Euskadi (Spain), Department of Chemistry, University of California, Berkeley and Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Department of Chemistry, Dalhousie University, Halifax, N.S., B3H 4J3 Canada
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Nienhaus K, Deng P, Kriegl JM, Nienhaus GU. Structural dynamics of myoglobin: effect of internal cavities on ligand migration and binding. Biochemistry 2003; 42:9647-58. [PMID: 12911306 DOI: 10.1021/bi034788k] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of sperm whale carbonmonoxy myoglobin (MbCO) after photodissociation. Photoproduct intermediates, characterized by CO in different locations, were selectively enhanced by laser illumination at specific temperatures. Measurements were performed on the wild-type protein and a series of mutants (L104W, I107W, I28F, and I28W) in which bulky amino acid side chains were introduced to block passageways between cavities or to fill these sites. Binding of xenon was also employed as an alternative means of filling cavities. In all samples, photolyzed CO ligands were observed to initially bind at primary docking site B in the vicinity of the heme iron, from where they migrate to the secondary docking sites, the Xe4 and/or Xe1 cavities. To examine the relevance of these internal docking sites for physiological ligand binding, we have performed room-temperature flash photolysis on the entire set of proteins in the CO- and O(2)-bound form. Together with the cryospectroscopic results, these data provide a clear picture of the role of the internal sites for ligand escape from and binding to myoglobin.
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Affiliation(s)
- Karin Nienhaus
- Department of Biophysics, University of Ulm, 89069 Ulm, Germany
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49
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Nienhaus K, Deng P, Kriegl JM, Nienhaus GU. Structural dynamics of myoglobin: spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W. Biochemistry 2003; 42:9633-46. [PMID: 12911305 DOI: 10.1021/bi034787s] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have studied CO binding to the heme and CO migration among protein internal cavities after photodissociation in sperm whale carbonmonoxy myoglobin (MbCO) mutant L29W using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) and kinetic experiments at cryogenic temperatures. Photoproduct intermediates, characterized by CO at particular locations in the protein, were selectively enhanced by applying special laser illumination protocols. These studies were performed on the L29W mutant protein and a series of double mutants constructed so that bulky amino acid side chains block passageways between cavities or fill these sites. Binding of xenon was also employed as an alternative means of occluding cavities. All mutants exhibit two conformations, A(I) and A(II), with distinctly different photoproduct states and ligand binding properties. These differences arise mainly from different positions of the W29 and H64 side chains in the distal heme pocket [Ostermann, A., et al. (2000) Nature 404, 205-208]. The detailed knowledge of the interplay between protein structure, protein dynamics, and ligand migration at cryogenic temperatures allowed us to develop a dynamic model that explains the slow CO and O(2) bimolecular association observed after flash photolysis at ambient temperature.
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Affiliation(s)
- Karin Nienhaus
- Department of Biophysics, University of Ulm, 89069 Ulm, Germany
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50
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Frauenfelder H, McMahon BH, Fenimore PW. Myoglobin: the hydrogen atom of biology and a paradigm of complexity. Proc Natl Acad Sci U S A 2003; 100:8615-7. [PMID: 12861080 PMCID: PMC166357 DOI: 10.1073/pnas.1633688100] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- H Frauenfelder
- Center for Nonlinear Studies, MS B258, and Theoretical Biology and Biophysics Group (T-10), MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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