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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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2
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Amadei A, Aschi M. Stationary and Time-Dependent Carbon Monoxide Stretching Mode Features in Carboxy Myoglobin: A Theoretical-Computational Reappraisal. J Phys Chem B 2021; 125:13624-13634. [PMID: 34904432 DOI: 10.1021/acs.jpcb.1c05815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The stationary and time-dependent infrared spectrum (IR) of the CO stretching mode (νCO) in carboxymyoglobin (MbCO), a longstanding problem of biophysical chemistry, has been modeled through a theoretical-computational method specifically designed for simulating quantum observables in complex atomic-molecular systems and based on a combined application of long time scale molecular dynamics simulations and quantum-chemical calculations. This study is basically focused on two aspects: (i) the origin of the stationary IR substates (termed as A0, A1, and A3) and (ii) the modeling and the interpretation of the νCO energy relaxation. The results, strengthened by a more than satisfactory agreement with the experimental data, concisely indicate that (i) the conformational His64-FeCO relevant substates, i.e., characterized by the formation-disruption of the H-bond between the above moieties, are the main responsible of the presence of two distinct and well separated (A0 and A1/A3) spectroscopic regions; (ii) the characteristic bimodal shape of the A1/A3 spectral region, according to our model, is the result of the fluctuation of the electric field pattern as provided by the protein-solvent framework perturbing the bound His64-CO-Heme complex; and (iii) the electric field pattern, in conjunction with the relatively high density of MbCO vibrational states, is also the main determinant of the νCO energy relaxation, characterizing its kinetic efficiency.
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Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", via della Ricerca Scientifica 1, 00 133 Roma, Italia
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università de l'Aquila, via Vetoio (Coppito 1), 67 010 l'Aquila, Italia
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3
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Roose BW, Zemerov SD, Dmochowski IJ. Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR. Methods Enzymol 2018; 602:249-272. [PMID: 29588032 DOI: 10.1016/bs.mie.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The physiological activity of xenon has long been recognized, though the exact nature of its interactions with biomolecules remains poorly understood. Xe is an inert noble gas, but can act as a general anesthetic, most likely by binding internal hydrophobic cavities within proteins. Understanding Xe-protein interactions, therefore, can provide crucial insight regarding the mechanism of Xe anesthesia and potentially other general anesthetic agents. Historically, Xe-protein interactions have been studied primarily through X-ray crystallography and nuclear magnetic resonance (NMR). In this chapter, we first describe our methods for preparing Xe derivatives of protein crystals and identifying Xe-binding sites. Second, we detail our procedure for 129Xe hyper-CEST NMR spectroscopy, a versatile NMR technique well suited for characterizing the weak, transient nature of Xe-protein interactions.
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4
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Lábas A, Menyhárd DK, Harvey JN, Oláh J. First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO. Chemistry 2018; 24:5350-5358. [PMID: 29285802 DOI: 10.1002/chem.201704867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2 , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.
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Affiliation(s)
- Anikó Lábas
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, H-1117, Budapest, Pázmány Péter st. 1/A, Hungary
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001, Leuven Celestijnenlaan 200F- box 2404, Belgium
| | - Julianna Oláh
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
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5
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Tian R, Losilla M, Lu Y, Yang G, Zakon H. Molecular evolution of globin genes in Gymnotiform electric fishes: relation to hypoxia tolerance. BMC Evol Biol 2017; 17:51. [PMID: 28193153 PMCID: PMC5307702 DOI: 10.1186/s12862-017-0893-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nocturnally active gymnotiform weakly electric fish generate electric signals for communication and navigation, which can be energetically taxing. These fish mainly inhabit the Amazon basin, where some species prefer well-oxygenated waters and others live in oxygen-poor, stagnant habitats. The latter species show morphological, physiological, and behavioral adaptations for hypoxia-tolerance. However, there have been no studies of hypoxia tolerance on the molecular level. Globins are classic respiratory proteins. They function principally in oxygen-binding and -delivery in various tissues and organs. Here, we investigate the molecular evolution of alpha and beta hemoglobins, myoglobin, and neuroglobin in 12 gymnotiforms compared with other teleost fish. RESULTS The present study identified positively selected sites (PSS) on hemoglobin (Hb) and myoglobin (Mb) genes using different maximum likelihood (ML) methods; some PSS fall in structurally important protein regions. This evidence for the positive selection of globin genes suggests that the adaptive evolution of these genes has helped to enhance the capacity for oxygen storage and transport. Interestingly, a substitution of a Cys at a key site in the obligate air-breathing electric eel (Electrophorus electricus) is predicted to enhance oxygen storage of Mb and contribute to NO delivery during hypoxia. A parallel Cys substitution was also noted in an air-breathing African electric fish (Gymnarchus niloticus). Moreover, the expected pattern under normoxic conditions of high expression of myoglobin in heart and neuroglobin in the brain in two hypoxia-tolerant species suggests that the main effect of selection on these globin genes is on their sequence rather than their basal expression patterns. CONCLUSION Results indicate a clear signature of positive selection in the globin genes of most hypoxia-tolerant gymnotiform fishes, which are obligate or facultative air breathers. These findings highlight the critical role of globin genes in hypoxia tolerance evolution of Gymnotiform electric fishes.
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Affiliation(s)
- Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- Department of Integrative Biology, The University of Texas, Austin, TX, 78759, USA
| | - Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ying Lu
- Department of Integrative Biology, The University of Texas, Austin, TX, 78759, USA
- Department of Neuroscience, The University of Texas, Austin, TX, 78759, USA
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.
| | - Harold Zakon
- Department of Integrative Biology, The University of Texas, Austin, TX, 78759, USA.
- Department of Neuroscience, The University of Texas, Austin, TX, 78759, USA.
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6
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Ascenzi P, di Masi A, Leboffe L, Fiocchetti M, Nuzzo MT, Brunori M, Marino M. Neuroglobin: From structure to function in health and disease. Mol Aspects Med 2016; 52:1-48. [DOI: 10.1016/j.mam.2016.10.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
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7
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Morrill GA, Kostellow AB. Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement. Front Physiol 2016; 7:360. [PMID: 27656147 PMCID: PMC5011150 DOI: 10.3389/fphys.2016.00360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/08/2016] [Indexed: 02/02/2023] Open
Abstract
Globins contain one or more cavities that control or affect such functions as ligand movement and ligand binding. Here we report that the extended globin family [cytoglobin (Cygb); neuroglobin (Ngb); myoglobin (Mb); hemoglobin (Hb) subunits Hba(α); and Hbb(β)] contain either a transmembrane (TM) helix or pore-lining region as well as internal cavities. Protein motif/domain analyses indicate that Ngb and Hbb each contain 5 cholesterol- binding (CRAC/CARC) domains and 1 caveolin binding motif, whereas the Cygb dimer has 6 cholesterol-binding domains but lacks caveolin-binding motifs. Mb and Hba each exhibit 2 cholesterol-binding domains and also lack caveolin-binding motifs. The Hb αβ-tetramer contains 14 cholesterol-binding domains. Computer algorithms indicate that Cygb and Ngb cavities display multiple partitions and C-terminal pore-lining regions, whereas Mb has three major cavities plus a C-terminal pore-lining region. The Hb tetramer exhibits a large internal cavity but the subunits differ in that they contain a C-terminal TM helix (Hba) and pore-lining region (Hbb). The cavities include 43 of 190 Cygb residues, 38 of 151 of Ngb residues, 55 of 154 Mb residues, and 137 of 688 residues in the Hb tetramer. Each cavity complex includes 6 to 8 residues of the TM helix or pore-lining region and CRAC/CARC domains exist within all cavities. Erythrocyte Hb αβ-tetramers are largely cytosolic but also bind to a membrane anion exchange protein, "band 3," which contains a large internal cavity and 12 TM helices (5 being pore-lining regions). The Hba TM helix may be the erythrocyte membrane "band 3" attachment site. "Band 3" contributes 4 caveolin binding motifs and 10 CRAC/CARC domains. Cholesterol binding may create lipid-disordered phases that alter globin cavities and facilitate ligand movement, permitting ion channel formation and conformational changes that orchestrate anion and ligand (O2, CO2, NO) movement within the large internal cavities and channels of the globins.
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Affiliation(s)
- Gene A Morrill
- Department of Physiology and Biophysics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Adele B Kostellow
- Department of Physiology and Biophysics, Albert Einstein College of Medicine Bronx, NY, USA
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8
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Borrelli KW, Vitalis A, Alcantara R, Guallar V. PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique. J Chem Theory Comput 2015; 1:1304-11. [PMID: 26631674 DOI: 10.1021/ct0501811] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combining protein structure prediction algorithms and Metropolis Monte Carlo techniques, we provide a novel method to explore all-atom energy landscapes. The core of the technique is based on a steered localized perturbation followed by side-chain sampling as well as minimization cycles. The algorithm and its application to ligand diffusion are presented here. Ligand exit pathways are successfully modeled for different systems containing ligands of various sizes: carbon monoxide in myoglobin, camphor in cytochrome P450cam, and palmitic acid in the intestinal fatty-acid-binding protein. These initial applications reveal the potential of this new technique in mapping millisecond-time-scale processes. The computational cost associated with the exploration is significantly less than that of conventional MD simulations.
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Affiliation(s)
- Kenneth W Borrelli
- Department of Biochemistry, Washington University School of Medicine, St Louis, Missouri 63108
| | - Andreas Vitalis
- Department of Biochemistry, Washington University School of Medicine, St Louis, Missouri 63108
| | - Raul Alcantara
- Department of Biochemistry, Washington University School of Medicine, St Louis, Missouri 63108
| | - Victor Guallar
- Department of Biochemistry, Washington University School of Medicine, St Louis, Missouri 63108
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9
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Morrison CN, Hoy JA, Zhang L, Einsle O, Rees DC. Substrate pathways in the nitrogenase MoFe protein by experimental identification of small molecule binding sites. Biochemistry 2015; 54:2052-60. [PMID: 25710326 PMCID: PMC4590346 DOI: 10.1021/bi501313k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
In
the nitrogenase molybdenum-iron (MoFe) protein, we have identified
five potential substrate access pathways from the protein surface
to the FeMo-cofactor (the active site) or the P-cluster using experimental
structures of Xe pressurized into MoFe protein crystals from Azotobacter vinelandii and Clostridium pasteurianum. Additionally, all published structures of the MoFe protein, including
those from Klebsiella pneumoniae, were analyzed for
the presence of nonwater, small molecules bound to the protein interior.
Each pathway is based on identification of plausible routes from buried
small molecule binding sites to both the protein surface and a metallocluster.
Of these five pathways, two have been previously suggested as substrate
access pathways. While the small molecule binding sites are not conserved
among the three species of MoFe protein, residues lining the pathways
are generally conserved, indicating that the proposed pathways may
be accessible in all three species. These observations imply that
there is unlikely a unique pathway utilized for substrate access from
the protein surface to the active site; however, there may be preferred
pathways such as those described here.
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Affiliation(s)
- Christine N Morrison
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Julie A Hoy
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Limei Zhang
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States
| | - Oliver Einsle
- ‡Institut für Biochemie and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Douglas C Rees
- †Division of Chemistry and Chemical Engineering, California Institute of Technology 114-96, Pasadena, California 91125, United States.,§Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, United States
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10
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Shelby ML, Mara MW, Chen LX. New insight into metalloporphyrin excited state structures and axial ligand binding from X-ray transient absorption spectroscopic studies. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.05.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Woods KN. Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity. SOFT MATTER 2014; 10:4387-4402. [PMID: 24801988 DOI: 10.1039/c3sm53229a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this investigation we use THz time-scale spectroscopy to conduct an initial set of studies on myoglobin with the aim of providing further insight into the global, collective thermal fluctuations in the protein that have been hypothesized to play a prominent role in the dynamic formation of transient ligand channels as well as in shaping the molecular level basis for ligand discrimination. Using the two ligands O2 and CO, we have determined that the perturbation from the heme-ligand complex has a strong influence on the characteristics of the myoglobin collective dynamics that are excited upon binding. Further, the differences detected in the collective protein motions in Mb-O2 compared with those in Mb-CO appear to be intimately tied with the pathways of long-range allosteric communication in the protein, which ultimately determine the trajectories selected by the respective ligands on the path to and from the heme-binding cavity.
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Affiliation(s)
- K N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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12
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Stickrath AB, Mara MW, Lockard JV, Harpham MR, Huang J, Zhang X, Attenkofer K, Chen LX. Detailed Transient Heme Structures of Mb-CO in Solution after CO Dissociation: An X-ray Transient Absorption Spectroscopic Study. J Phys Chem B 2012; 117:4705-12. [DOI: 10.1021/jp3086705] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew B. Stickrath
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Michael W. Mara
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
| | - Jenny V. Lockard
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Michael R. Harpham
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Jier Huang
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Xiaoyi Zhang
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Klaus Attenkofer
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Lin X. Chen
- Chemical Sciences
and Engineering Division and X-ray Sciences Division,
Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Chemistry, Northwestern University, 2145 Sheridan
Road, Evanston, Illinois 60208, United States
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13
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Thielges MC, Fayer MD. Protein dynamics studied with ultrafast two-dimensional infrared vibrational echo spectroscopy. Acc Chem Res 2012; 45:1866-74. [PMID: 22433178 DOI: 10.1021/ar200275k] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins, enzymes, and other biological molecules undergo structural dynamics as an intrinsic part of their biological functions. While many biological processes occur on the millisecond, second, and even longer time scales, the fundamental structural dynamics that eventually give rise to such processes occur on much faster time scales. Many decades ago, chemical kineticists focused on the inverse of the reaction rate constant as the important time scale for a chemical reaction. However, through transition state theory and a vast amount of experimental evidence, we now know that the key events in a chemical reaction can involve structural fluctuations that take a system of reactants to its transition state, the crossing of a barrier, and the eventual relaxation to product states. Such dynamics occur on very fast time scales. Today researchers would like to investigate the fast structural fluctuations of biological molecules to gain an understanding of how biological processes proceed from simple structural changes in biomolecules to the final, complex biological function. The study of the fast structural dynamics of biological molecules requires experiments that operate on the appropriate time scales, and in this Account, we discuss the application of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy to the study of protein dynamics. The 2D IR vibrational echo experiment is akin to 2D NMR, but it operates on time scales many orders of magnitude faster. In the experiments, a particular vibrational oscillator serves as a vibrational dynamics probe. As the structure of the protein evolves in time, the structural changes are manifested as time-dependent changes in the frequency of the vibrational dynamics probe. The 2D IR vibrational echo experiments can track the vibrational frequency evolution, which we then relate to the time evolution of the protein structure. In particular, we measured protein substate interconversion for mutants of myoglobin using 2D IR chemical exchange spectroscopy and observed well-defined substate interconversion on a sub-100 ps time scale. In another study, we investigated the influence of binding five different substrates to the enzyme cytochrome P450(cam). The various substrates affect the enzyme dynamics differently, and the observed dynamics are correlated with the enzyme's selectivity of hydroxylation of the substrates and with the substrate binding affinity.
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Affiliation(s)
- Megan C. Thielges
- Department of Chemistry Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry Stanford University, Stanford, California 94305, United States
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14
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Dynamics comparison of two myoglobins with a distinct heme active site. J Mol Model 2011; 18:1591-6. [DOI: 10.1007/s00894-011-1192-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
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15
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Lin TL, Song G. Efficient mapping of ligand migration channel networks in dynamic proteins. Proteins 2011; 79:2475-90. [DOI: 10.1002/prot.23071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/01/2011] [Accepted: 04/19/2011] [Indexed: 11/07/2022]
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16
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Thielges MC, Chung JK, Fayer MD. Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy. J Am Chem Soc 2011; 133:3995-4004. [PMID: 21348488 PMCID: PMC3063108 DOI: 10.1021/ja109168h] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.
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Affiliation(s)
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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17
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Bagchi S, Nebgen BT, Loring RF, Fayer MD. Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations. J Am Chem Soc 2010; 132:18367-76. [PMID: 21142083 PMCID: PMC3033732 DOI: 10.1021/ja108491t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Myoglobin (Mb) double mutant T67R/S92D displays peroxidase enzymatic activity in contrast to the wild type protein. The CO adduct of T67R/S92D shows two CO absorption bands corresponding to the A(1) and A(3) substates. The equilibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by using two-dimensional infrared (2D IR) vibrational echo spectroscopy and molecular dynamics (MD) simulations. The time-dependent changes in the 2D IR vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS) method to obtain the frequency-frequency correlation function (FFCF). The results for the double mutant are compared to those from the wild type Mb. The experimentally determined FFCF is compared to the FFCF obtained from molecular dynamics simulations, thereby testing the capacity of a force field to determine the amplitudes and time scales of protein structural fluctuations on fast time scales. The results provide insights into the nature of the energy landscape around the free energy minimum of the folded protein structure.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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18
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Bagchi S, Thorpe DG, Thorpe IF, Voth GA, Fayer MD. Conformational switching between protein substates studied with 2D IR vibrational echo spectroscopy and molecular dynamics simulations. J Phys Chem B 2010; 114:17187-93. [PMID: 21128650 DOI: 10.1021/jp109203b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Myoglobin is an important protein for the study of structure and dynamics. Three conformational substates have been identified for the carbonmonoxy form of myoglobin (MbCO). These are manifested as distinct peaks in the IR absorption spectrum of the CO stretching mode. Ultrafast 2D IR vibrational echo chemical exchange experiments are used to observed switching between two of these substates, A(1) and A(3), on a time scale of <100 ps for two mutants of wild-type Mb. The two mutants are a single mutation of Mb, L29I, and a double mutation, T67R/S92D. Molecular dynamics (MD) simulations are used to model the structural differences between the substates of the two MbCO mutants. The MD simulations are also employed to examine the substate switching in the two mutants as a test of the ability of MD simulations to predict protein dynamics correctly for a system in which there is a well-defined transition over a significant potential barrier between two substates. For one mutant, L29I, the simulations show that translation of the His64 backbone may differentiate the two substates. The simulations accurately reproduce the experimentally observed interconversion time for the L29I mutant. However, MD simulations exploring the same His64 backbone coordinate fail to display substate interconversion for the other mutant, T67R/S92D, thus pointing to the likely complexity of the underlying protein interactions. We anticipate that understanding conformational dynamics in MbCO via ultrafast 2D IR vibrational echo chemical exchange experiments can help to elucidate fast conformational switching processes in other proteins.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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19
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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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20
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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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21
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Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M. Breathing motions of a respiratory protein revealed by molecular dynamics simulations. J Am Chem Soc 2009; 131:11825-32. [PMID: 19653680 DOI: 10.1021/ja9028473] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Internal cavities, which are central to the biological functions of myoglobin, are exploited by gaseous ligands (e.g., O(2), NO, CO, etc.) to migrate inside the protein matrix. At present, it is not clear whether the ligand makes its own way inside the protein or instead the internal cavities are an intrinsic feature of myoglobin. To address this issue, standard molecular dynamics simulations were performed on horse-heart met-myoglobin with no ligand migrating inside the protein matrix. To reveal intrinsic internal pathways, the use of a statistical approach was applied to the cavity calculation, with special emphasis on the major pathway from the distal pocket to Xe1. Our study points out the remarkable dynamical behavior of Xe4, whose "breathing motions" may facilitate migration of ligands through the distal region. Additionally, our results highlight a two-way path for a ligand to diffuse through the proximal region, possibly allowing an alternative route in case Xe1 is occupied. Finally, our approach has led us to the identification of key residues, such as leucines, that may work as switches between cavities.
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Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Chemical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (Ca), Italy
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22
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Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:327-36. [PMID: 19826803 DOI: 10.1007/s00249-009-0551-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 09/09/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022]
Abstract
Extradiol dioxygenases facilitate microbial aerobic degradation of catechol and its derivatives by activating molecular dioxygen and incorporating both oxygen atoms into their substrates. Experimental and theoretical studies have focused on the mechanism of the reaction at the active site. However, whether the catalytic rate is limited by O(2) access to the active site has not yet been explored. Here, we choose a recently solved X-ray structure of homoprotocatechuate 2,3-dioxygenase as a typical example to determine potential pathways for O(2) migration from the solvent into the enzyme center. On the basis of the trajectories of two 10-ns molecular dynamics simulations, implicit ligand sampling was used to calculate the 3D free energy map for O(2) inside the protein. The energetically optimal routes for O(2) diffusion were identified for each subunit of the homotetrameric protein structure. The O(2) tunnels formed because of thermal fluctuations were also characterized by connecting elongated cavities inside the protein. By superimposing the favorable O(2) tunnels on to the free energy map, both energetically and geometrically preferred O(2) pathways were determined, as also were the amino acids that may be critical for O(2) passage along these paths. Our results demonstrate that identical subunits possess quite distinct O(2) tunnels. The order of O(2) affinity of these tunnels is generally consistent with the order of the catalytic rate of each subunit. As a consequence, the probability of finding the reaction product is highest in the subunit containing the highest O(2) affinity pathway.
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23
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Xu L, Liu X, Zhao W, Wang X. Locally Enhanced Sampling Study of Dioxygen Diffusion Pathways in Homoprotocatechuate 2,3-Dioxygenase. J Phys Chem B 2009; 113:13596-603. [DOI: 10.1021/jp902597t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liang Xu
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Xin Liu
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Weijie Zhao
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Xicheng Wang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
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24
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Klvana M, Pavlova M, Koudelakova T, Chaloupkova R, Dvorak P, Prokop Z, Stsiapanava A, Kuty M, Kuta-Smatanova I, Dohnalek J, Kulhanek P, Wade RC, Damborsky J. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations. J Mol Biol 2009; 392:1339-56. [PMID: 19577578 DOI: 10.1016/j.jmb.2009.06.076] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 06/25/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
Abstract
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, and exchange pathways for water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c, and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1, whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen-bonding interactions with the active-site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product, and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel, and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.
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Affiliation(s)
- Martin Klvana
- Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic
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25
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Fayer M. Dynamics of Liquids, Molecules, and Proteins Measured with Ultrafast 2D IR Vibrational Echo Chemical Exchange Spectroscopy. Annu Rev Phys Chem 2009; 60:21-38. [PMID: 18851709 DOI: 10.1146/annurev-physchem-073108-112712] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M.D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305;
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26
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Orlowski S, Nowak W. Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin. Biosystems 2008; 94:263-6. [DOI: 10.1016/j.biosystems.2008.04.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 04/18/2008] [Indexed: 11/15/2022]
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27
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Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin. Proc Natl Acad Sci U S A 2008; 105:9204-9. [PMID: 18599444 DOI: 10.1073/pnas.0710825105] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myoglobin is a globular protein involved in oxygen storage and transport. No consensus yet exists on the atomic level mechanism by which oxygen and other small nonpolar ligands move between the myoglobin's buried heme, which is the ligand binding site, and surrounding solvent. This study uses room temperature molecular dynamics simulations to provide a complete atomic level picture of ligand migration in myoglobin. Multiple trajectories--providing a cumulative total of 7 micros of simulation--are analyzed. Our simulation results are consistent with and tie together previous experimental findings. Specifically, we characterize: (i) Explicit full trajectories in which the CO ligand shuttles between the internal binding site and the solvent and (ii) pattern and structural origins of transient voids available for ligand migration. The computations are performed both in sperm whale myoglobin wild-type and in sperm whale V68F myoglobin mutant, which is experimentally known to slow ligand-binding kinetics. On the basis of these independent, but mutually consistent ligand migration and transient void computations, we find that there are two discrete dynamical pathways for ligand migration in myoglobin. Trajectory hops between these pathways are limited to two bottleneck regions. Ligand enters and exits the protein matrix in common identifiable portals on the protein surface. The pathways are located in the "softer" regions of the protein matrix and go between its helices and in its loop regions. Localized structural fluctuations are the primary physical origin of the simulated CO migration pathways inside the protein.
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28
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Abstract
Folded proteins can exist in multiple conformational substates. Each substate reflects a local minimum on the free-energy landscape with a distinct structure. By using ultrafast 2D-IR vibrational echo chemical-exchange spectroscopy, conformational switching between two well defined substates of a myoglobin mutant is observed on the approximately 50-ps time scale. The conformational dynamics are directly measured through the growth of cross peaks in the 2D-IR spectra of CO bound to the heme active site. The conformational switching involves motion of the distal histidine/E helix that changes the location of the imidazole side group of the histidine. The exchange between substates changes the frequency of the CO, which is detected by the time dependence of the 2D-IR vibrational echo spectrum. These results demonstrate that interconversion between protein conformational substates can occur on very fast time scales. The implications for larger structural changes that occur on much longer time scales are discussed.
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29
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Kondrashov DA, Zhang W, Aranda R, Stec B, Phillips GN. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins 2008; 70:353-62. [PMID: 17680690 DOI: 10.1002/prot.21499] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a range of crystallization conditions, often resulting in different space groups and changes in the packing arrangements. Three high resolution structures of myoglobin (Mb) in different crystal space groups are presented, including one in a new space group P6(1)22 and two structures in space groups P2(1)2(1)2(1) and P6. We compare coordinates and anisotropic displacement parameters (ADPs) from these three structures plus an existing structure in space group P2(1). While the overall changes are small, there is substantial variation in several external regions with varying patterns of crystal contacts across the space group packing arrangements. The structural ensemble containing four different crystal forms displays greater conformational variance (Calpha rmsd of 0.54-0.79 A) in comparison to a collection of four Mb structures with different ligands and mutations in the same crystal form (Calpha rmsd values of 0.28-0.37 A). The high resolution of the data enables comparison of both the magnitudes and directions of ADPs, which are found to be suppressed by crystal contacts. A composite dynamic profile of Mb structural variation from the four structures was compared with an independent structural ensemble developed from NMR refinement. Despite the limitations and biases of each method, the ADPs of the crystallographic ensemble closely match the positional variance from the solution NMR ensemble with linear correlation of 0.8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure.
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Affiliation(s)
- Dmitry A Kondrashov
- Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, USA
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30
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31
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Samuni U, Dantsker D, Roche C, Friedman JM. Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins. Gene 2007; 398:234-48. [PMID: 17570619 PMCID: PMC1975397 DOI: 10.1016/j.gene.2007.04.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ligand recombination studies play a central role both for characterizing different hemeproteins and their conformational states but also for probing fundamental biophysical processes. Consequently, there is great importance to providing a foundation from which one can understand the physical processes that give rise to and modulate the large range of kinetic patterns associated with ligand recombination in myoglobins and hemoglobins. In this work, an overview of cryogenic and solution phase recombination phenomena for COMb is first reviewed and then a new paradigm is presented for analyzing the temperature and viscosity dependent features of kinetic traces in terms of multiple phases that reflect which tier(s) of solvent slaved protein dynamics is (are) operative on the photoproduct population during the time course of the measurement. This approach allows for facile inclusion of both ligand diffusion among accessible cavities and conformational relaxation effects. The concepts are illustrated using kinetic traces and MEM populations derived from the CO recombination process for wild type and mutant myoglobins either in sol-gel matrices bathed in glycerol or in trehalose-derived glassy matrices.
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Affiliation(s)
- Uri Samuni
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - David Dantsker
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - Camille Roche
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - Joel M. Friedman
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
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32
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Orlowski S, Nowak W. Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. J Mol Model 2007; 13:715-23. [PMID: 17503097 DOI: 10.1007/s00894-007-0203-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 03/20/2007] [Indexed: 11/28/2022]
Abstract
Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.
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Affiliation(s)
- Slawomir Orlowski
- Theoretical Molecular Biophysics Group, Institute of Physics, Nicolaus Copernicus University, ul. Grudziadzka 5, 87-100, Torun, Poland
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33
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Mouawad L, Tetreau C, Abdel-Azeim S, Perahia D, Lavalette D. CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations. Protein Sci 2007; 16:781-94. [PMID: 17400927 PMCID: PMC2206643 DOI: 10.1110/ps.062374707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450(cam)(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450(cam)(cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics.
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Affiliation(s)
- Liliane Mouawad
- Inserm U759, Institut Curie-Recherche, Bâtiment 112, Université Paris-Sud, 91405 Orsay cedex, France.
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34
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Youngblood B, Shieh FK, De Los Rios S, Perona JJ, Reich NO. Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI. J Mol Biol 2006; 362:334-46. [PMID: 16919299 DOI: 10.1016/j.jmb.2006.07.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 07/01/2006] [Accepted: 07/14/2006] [Indexed: 11/19/2022]
Abstract
Improved sequence specificity of the DNA cytosine methyltransferase HhaI was achieved by disrupting interactions at a hydrophobic interface between the active site of the enzyme and a highly conserved flexible loop. Transient fluorescence experiments show that mutations disrupting this interface destabilize the positioning of the extrahelical, "flipped" cytosine base within the active site. The ternary crystal structure of the F124A M.HhaI bound to cognate DNA and the cofactor analogue S-adenosyl-l-homocysteine shows an increase in cavity volume between the flexible loop and the core of the enzyme. This cavity disrupts the interface between the loop and the active site, thereby destabilizing the extrahelical target base. The favored partitioning of the base-flipped enzyme-DNA complex back to the base-stacked intermediate results in the mutant enzyme discriminating better than the wild-type enzyme against non-cognate sites. Building upon the concepts of kinetic proofreading and our understanding of M.HhaI, we describe how a 16-fold specificity enhancement achieved with a double mutation at the loop/active site interface is acquired through destabilization of intermediates prior to methyltransfer rather than disruption of direct interactions between the enzyme and the substrate for M.HhaI.
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Affiliation(s)
- Ben Youngblood
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106-9510, USA
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35
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Oxygen diffusion in minihemoglobin from Cerebratulus lacteus: a locally enhanced sampling study. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0139-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Sottini S, Abbruzzetti S, Spyrakis F, Bettati S, Ronda L, Mozzarelli A, Viappiani C. Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets. J Am Chem Soc 2006; 127:17427-32. [PMID: 16332093 DOI: 10.1021/ja056101k] [Citation(s) in RCA: 28] [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
Biphasic geminate rebinding of CO to myoglobin upon flash photolysis has been associated to ligand distribution in hydrophobic cavities, structurally detected by time-resolved crystallography, xenon occupancy, and molecular simulations. We show that the time course of CO rebinding to human hemoglobin also exhibits a biphasic geminate rebinding when the protein is entrapped in wet nanoporous silica gel. A simple branched kinetic scheme, involving the bound state A, the primary docking site C, and a secondary binding site B was used to calculate the microscopic rates and the time-dependent population of the intermediate species. The activation enthalpies of the associated transitions were determined in the absence and presence of 80% glycerol. Potential hydrophobic docking cavities within the alpha and beta chains of hemoglobin were identified by computational modeling using xenon as a probe. A hydrophobic pocket on the distal side of the heme, corresponding to Xe4 in Mb, and a nearby site that does not have a correspondence in Mb were detected. Neither potential xenon sites on the proximal side nor a migration channel from the distal to proximal site was located. The small enthalpic barriers between states B and C are in very good agreement with the location of the xenon sites on the distal side. Furthermore, the connection between the two xenon sites is relatively open, explaining why the decreased mobility of the protein with viscosity only slightly perturbs the energetics of ligand migration between the two sites.
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Affiliation(s)
- Silvia Sottini
- Dipartimento di Fisica, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy
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37
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Abstract
We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides Calphas for all residues but glycines in the coarse-graining procedure, without leading to an increase in the degrees of freedom (beta Gaussian Model). Normalized covariance matrix and deformation along slowest modes with collective character are analyzed, pointing out anticorrelations between functionally relevant sites for the proteins under study. In particular, we underline the functional motions of an extended tunnel-cavity system running inside the protein matrix, which provide a pathway for small ligands binding with the iron in the heme group. We give a rough estimate of the order of magnitude of the relaxation times of the slowest two overdamped modes and compare results with previous studies on globins.
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Affiliation(s)
- Luca Marsella
- International School for Advanced Studies (S.I.S.S.A.), Trieste, Italy.
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38
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Hamdane D, Kiger L, Hoa GHB, Dewilde S, Uzan J, Burmester T, Hankeln T, Moens L, Marden MC. High Pressure Enhances Hexacoordination in Neuroglobin and Other Globins. J Biol Chem 2005; 280:36809-14. [PMID: 16100391 DOI: 10.1074/jbc.m506253200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The techniques of high applied pressure and flash photolysis have been combined to study ligand rebinding to neuroglobin (Ngb) and tomato Hb, globins that may display a His-Fe-His hexacoordination in the absence of external ligands. High pressure induces a moderate decrease in the His association rate and a large decrease in His dissociation rate, thus leading to an enhancement of the overall His affinity. The overall structural difference between penta- and hexacoordinated globins may be rather small and can be overcome by external modifications such as high pressure. Over the pressure range 0.1-700 MPa (7 kbar), the globins may show a loss of over a factor of 100 in the amplitude of the bimolecular rebinding phase after photodissociation. The kinetic data show that pressure induces a moderate increase of the rate for ligand binding from the correlated pair state (just after photodissociation) and a large (factor of 1000) decrease in rate for migration through the protein. The effect on the ligand migration phase was similar for both the external ligands (such as oxygen) as for the internal (histidine) ligand, suggesting the dominant role of protein fluctuations, rather than specific chemical barriers. Thus high pressure efficiently closes the protein migration channels; however, contrary to the effect of high viscosity, high pressure induces a greater decrease in rate for ligand migration toward the exterior (heme to the solvent) versus inward migration, as if the presence of the ligand itself induces an additional steric constraint.
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Affiliation(s)
- Djemel Hamdane
- INSERM U473, 78 rue du General Leclerc, 94275 Le Kremlin-Bicêtre, France
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39
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Dantsker D, Roche C, Samuni U, Blouin G, Olson JS, Friedman JM. The Position 68(E11) Side Chain in Myoglobin Regulates Ligand Capture, Bond Formation with Heme Iron, and Internal Movement into the Xenon Cavities. J Biol Chem 2005; 280:38740-55. [PMID: 16155005 DOI: 10.1074/jbc.m506333200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After photodissociation, ligand rebinding to myoglobin exhibits complex kinetic patterns associated with multiple first-order geminate recombination processes occurring within the protein and a simpler bimolecular phase representing second-order ligand rebinding from the solvent. A smooth transition from cryogenic-like to solution phase properties can be obtained by using a combination of sol-gel encapsulation, addition of glycerol as a bathing medium, and temperature tuning (-15 --> 65 degrees C). This approach was applied to a series of double mutants, myoglobin CO (H64L/V68X, where X = Ala, Val, Leu, Asn, and Phe), which were designed to examine the contributions of the position 68(E11) side chain to the appearance and disappearance of internal rebinding phases in the absence of steric and polar interactions with the distal histidine. Based on the effects of viscosity, temperature, and the stereochemistry of the E11 side chain, the three major phases, B --> A, C --> A, and D --> A, can be assigned, respectively, to ligand rebinding from the following: (i) the distal heme pocket, (ii) the xenon cavities prior to large amplitude side chain conformational relaxation, and (iii) the xenon cavities after significant conformational relaxation of the position 68(E11) side chain. The relative amplitudes of the B --> A and C --> A phases depend markedly on the size and shape of the E11 side chain, which regulates sterically both ligand return to the heme iron atom and ligand migration to the xenon cavities. The internal xenon cavities provide a transient docking site that allows side chain relaxations and the entry of water into the vacated distal pocket, which in turn slows ligand recombination markedly.
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Affiliation(s)
- David Dantsker
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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40
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de Sanctis D, Dewilde S, Vonrhein C, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Ponassi M, Nardini M, Bolognesi M. Bishistidyl Heme Hexacoordination, a Key Structural Property in Drosophila melanogaster Hemoglobin. J Biol Chem 2005; 280:27222-9. [PMID: 15917230 DOI: 10.1074/jbc.m503814200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemoglobins at high concentration have been isolated long ago from some insect larvae living in hypoxic environments. Conversely, a monomeric hemoglobin has been discovered recently in the fruit fly Drosophila melanogaster as intracellular protein expressed both in larvae and in the adult fly. Such a finding indicates that the oxygen supply in insects may be more complex than previously thought, relying not only on O2 diffusion through the tubular tracheal system, but also on carrier-mediated transport and storage. We present here the crystal structure of recombinant D. melanogaster hemoglobin at 1.20 A resolution. Spectroscopic data show that the protein displays a hexacoordinated heme, whose axial ligands are the proximal and distal His residues. Such bis-His ligation of the heme has sizable effects on the protein local structure. Three protein matrix cavities, comparable in size but not in topological locations with those of sperm whale myoglobin, are spread through the protein matrix; one of these can host a xenon atom. Additionally, D. melanogaster hemoglobin binds one molecule of 3-(cyclohexylamino)propanesulfonic acid (CAPS) buffer at a surface pocket, next to the EF hinge. Despite the high resolution achieved, no sequence/structure features specifically supporting the heme hexa- to pentacoordination transition required for diatomic ligand binding could be recognized.
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Affiliation(s)
- Daniele de Sanctis
- Department of Physics, National Institute for the Physics of Matter (NFM), University of Genova, Genova I-16146, Italy
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41
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Duff AP, Trambaiolo DM, Cohen AE, Ellis PJ, Juda GA, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM. Using Xenon as a Probe for Dioxygen-binding Sites in Copper Amine Oxidases. J Mol Biol 2004; 344:599-607. [PMID: 15533431 DOI: 10.1016/j.jmb.2004.09.075] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Revised: 09/21/2004] [Accepted: 09/24/2004] [Indexed: 11/28/2022]
Abstract
Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site.
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Affiliation(s)
- Anthony P Duff
- School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
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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: 415] [Impact Index Per Article: 20.8] [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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