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Abstract
Hemoglobin (Hgb) forms tetramers (dimerized α-β dimers), which enhance its globular stability and may also facilitate small gas molecule transport, as shown by recent all-atom Newtonian solvated simulations. Hydropathic bioinformatic thermodynamic scaling enables close comparisons of hemoglobin dimers with myoglobin and neuroglobin, and reveals many nonlocal wave-like features of strained Hgb structures at the coarse-grained amino acid level. The thermodynamic analysis employs two hydropathic scales, one describing abrupt first-order unfolding transitions, the other continuous second-order transitions. Small molecule exchange at hemes is a first-order process. Wave-like collective tetrameric features appropriate to ligand absorption and release, seen in optical experiments (short times), are identified thermodynamically at long times. Strain fields localized near hemes interfere with extended strain fields associated with dimer interfacial misfit, resulting in novel wavelength dependent dimer correlation function Fano antiresonances.
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Affiliation(s)
- J C Phillips
- Department of Physics and Astronomy , Rutgers University , Piscataway , New Jersey 08854 , United States
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2
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Oang KY, Kim KH, Jo J, Kim Y, Kim JG, Kim TW, Jun S, Kim J, Ihee H. Sub-100-ps structural dynamics of horse heart myoglobin probed by time-resolved X-ray solution scattering. Chem Phys 2014; 422:137-142. [PMID: 25678733 PMCID: PMC4323384 DOI: 10.1016/j.chemphys.2014.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we report sub-100-ps structural dynamics of horse heart myoglobin revealed by time-resolved X-ray solution scattering. By applying the time-slicing scheme to the measurement and subsequent deconvolution, we investigate the protein structural dynamics that occur faster than the X-ray temporal pulse width of synchrotrons (~100 ps). The singular value decomposition analysis of the experimental data suggests that two structurally distinguishable intermediates are formed within 100 ps. In particular, the global structural change occurring on the time scale of 70 ps is identified.
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Affiliation(s)
- Key Young Oang
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Kyung Hwan Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Junbeom Jo
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Youngmin Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Jong Goo Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Tae Wu Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Sunhong Jun
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon 402-751, Republic of Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
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3
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Oang KY, Kim JG, Yang C, Kim TW, Kim Y, Kim K, Kim J, Ihee H. Conformational Substates of Myoglobin Intermediate Resolved by Picosecond X-ray Solution Scattering. J Phys Chem Lett 2014; 5:804-808. [PMID: 24761190 PMCID: PMC3985870 DOI: 10.1021/jz4027425] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/11/2014] [Indexed: 05/04/2023]
Abstract
Conformational substates of proteins are generally considered to play important roles in regulating protein functions, but an understanding of how they influence the structural dynamics and functions of the proteins has been elusive. Here, we investigate the structural dynamics of sperm whale myoglobin associated with the conformational substates using picosecond X-ray solution scattering. By applying kinetic analysis considering all of the plausible candidate models, we establish a kinetic model for the entire cycle of the protein transition in a wide time range from 100 ps to 10 ms. Four structurally distinct intermediates are formed during the cycle, and most importantly, the transition from the first intermediate to the second one (B → C) occurs biphasically. We attribute the biphasic kinetics to the involvement of two conformational substates of the first intermediate, which are generated by the interplay between the distal histidine and the photodissociated CO.
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Affiliation(s)
- Key Young Oang
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Jong Goo Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Cheolhee Yang
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Tae Wu Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Youngmin Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Kyung
Hwan Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Jeongho Kim
- Department
of Chemistry, Inha University, Incheon 402-751, Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
- E-mail:
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4
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Dadusc G, Goodno GD, Chiu HL, Ogilvie J, Miller RD. Advances in Grating-Based Photoacoustic Spectroscopy for the Study of Protein Dynamics. Isr J Chem 2013. [DOI: 10.1002/ijch.199800021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Terazima M. Ligand Dissociation Process from Myoglobin Monitored by the Time-Resolved Volume Change. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200600029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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6
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Kim J, Kim KH, Kim JG, Kim TW, Kim Y, Ihee H. Anisotropic Picosecond X-ray Solution Scattering from Photo-selectively Aligned Protein Molecules. J Phys Chem Lett 2011; 2:350-356. [PMID: 21643489 PMCID: PMC3106313 DOI: 10.1021/jz101503r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Anisotropic X-ray scattering patterns of transiently aligned protein molecules in solution are measured by using pump-probe X-ray solution scattering. When a linearly polarized laser pulse interacts with an ensemble of molecules, the population of excited molecules is created with their transition dipoles preferentially aligned along the laser polarization direction. We measured the X-ray scattering from the myoglobin protein molecules excited by a linearly polarized, short laser pulse and obtained anisotropic scattering patterns on 100 ps time scale. An anisotropic scattering pattern contains higher structural information content than a typical isotropic pattern available from randomly oriented molecules. In addition, multiple independent diffraction patterns measured by using various laser polarization orientations will give substantially increased amount of structural information compared with a single isotropic pattern. By monitoring the temporal change of the anisotropic scattering pattern from 100 ps to 1 μs, we observed the orientational dynamics of photo-generated myoglobin with the rotational diffusion time of ∼15 ns.
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7
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Kim KH, Oang KY, Kim J, Lee JH, Kim Y, Ihee H. Direct observation of myoglobin structural dynamics from 100 picoseconds to 1 microsecond with picosecond X-ray solution scattering. Chem Commun (Camb) 2010; 47:289-91. [PMID: 20733999 DOI: 10.1039/c0cc01817a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Here we report structural dynamics of equine myoglobin (Mb) in response to the CO photodissociation visualized by picosecond time-resolved X-ray solution scattering. The data clearly reveal new structural dynamics that occur in the timescale of ∼360 picoseconds (ps) and ∼9 nanoseconds (ns), which have not been clearly detected in previous studies.
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Affiliation(s)
- Kyung Hwan Kim
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Korea
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8
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Ihee H, Wulff M, Kim J, Adachi SI. Ultrafast X-ray scattering: structural dynamics from diatomic to protein molecules. INT REV PHYS CHEM 2010. [DOI: 10.1080/0144235x.2010.498938] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Harada M, Okamoto K, Terazima M. Diffusion of gold ions and gold particles during photoreduction processes probed by the transient grating method. J Colloid Interface Sci 2009; 332:373-81. [DOI: 10.1016/j.jcis.2008.12.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 12/15/2008] [Accepted: 12/17/2008] [Indexed: 10/21/2022]
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10
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Nakasone Y, Eitoku T, Matsuoka D, Tokutomi S, Terazima M. Dynamics of conformational changes of Arabidopsis phototropin 1 LOV2 with the linker domain. J Mol Biol 2007; 367:432-42. [PMID: 17275025 DOI: 10.1016/j.jmb.2006.12.074] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 12/14/2006] [Accepted: 12/29/2006] [Indexed: 11/30/2022]
Abstract
Conformational changes of Arabidopsis phot1-LOV2 with the linker (phot1-LOV2-linker) were investigated from the viewpoint of the changes in molecular volume and molecular diffusion coefficient (D) by time-resolved transient grating (TG) and transient lens (TrL) methods. Although the absorption spectrum change completes within a few microseconds, the D-value detected by the TG method decreased drastically with a time constant of 1.0 ms from 9.2(+/-0.4)x10(-11) m(2)/s to 5.0(+/-0.3)x10(-11) m(2)/s. This time-dependent D was interpreted in terms of the unfolding of alpha-helices in the linker region. The change of the alpha-helices was confirmed by observing the recovery of the circular dichroism intensity. The TrL signal showed that the molecular volume decreases with two time constants; 300 micros and 1.0 ms. The former time constant is close to the previously observed photo-dissociation reaction rate of the phot1-LOV2 (without the linker) dimer, and the latter one agrees well with the rate of the D-change. Considering a similar time constant of the dissociation reaction of the LOV2 dimer, we interpreted these kinetics in terms of the dissociation step of the linker region from the LOV2 domain (T(390)(pre) state). After this step, the protein volume and D are decreased significantly with the lifetime of 1.0 ms. The D decrease indicates the increase of the intermolecular interaction between the protein and water molecules. On the basis of these observations, a two-step mechanism of the linker unfolding is proposed.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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11
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Terazima M. Photothermal Studies of Photophysical and Photochemical Processes by the Transient Grating Method. ADVANCES IN PHOTOCHEMISTRY 2007. [DOI: 10.1002/9780470133552.ch5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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12
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Callender R, Dyer RB. Advances in Time-Resolved Approaches To Characterize the Dynamical Nature of Enzymatic Catalysis. Chem Rev 2006; 106:3031-42. [PMID: 16895316 DOI: 10.1021/cr050284b] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
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13
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Nishihara Y, Sakakura M, Kimura Y, Terazima M. The Escape Process of Carbon Monoxide from Myoglobin to Solution at Physiological Temperature. J Am Chem Soc 2004; 126:11877-88. [PMID: 15382923 DOI: 10.1021/ja038877w] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carbon monoxide (CO) docking sites involved in the ligand escape process from the iron atom in hem of myoglobin (Mb) to solution at physiological temperature were studied on the basis of the effect of xenon (Xe) on the ligand escape rate by the transient grating (TG) technique. The TG method provides a direct measurement of the changes in molecular volume. The apparent CO escaping rate and the volume contraction increase with increasing Xe pressure. The pressure dependence of the rate is consistent with that of the Xe population at the Xe(1) site. This result clearly shows that CO is trapped at the Xe(1) site before escaping to solvent in a Xe-free solution at room temperature. It is shown that only CO but not the trapped Xe is released by the photoexcitation of the Xe-trapped MbCO. A dissociation scheme is proposed to explain the enhancement of the escaping rate by the presence of Xe(1). There are two branches for the CO escaping pathway. The dominant part of the dissociated CO escapes to the solvent through the Xe(1) trapping site under the Xe-free condition, and there are at least three intermediate states along this pathway. When a Xe atom blocks the Xe(1) site, the CO escapes through another route.
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Affiliation(s)
- Yasutaka Nishihara
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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14
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Terazima M. Time-Resolved Thermodynamic Properties of Intermediate Species during Photochemical Reactions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.23] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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16
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Miyata R, Terazima M. Transient Thermal Expansion of a Protein in Solution after Photo-Excitation of the Chromophore: Deoxymyoglobin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2003. [DOI: 10.1246/bcsj.76.1707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Abstract
There have been recent advances in initiating and perturbing chemical reactions on very fast timescales, as short as picoseconds, thus making it feasible to study a vast range of chemical kinetics problems that heretofore could not be studied. One such approach is the rapid heating of water solutions using laser excitation. Laser-induced temperature jump relaxation spectroscopy can be used to determine the dynamics of protein motion, an area largely unstudied for want of suitable experimental and theoretical probes, despite the obvious importance of dynamics to protein function. Coupled with suitable spectroscopic probes of structure, relaxation spectroscopy can follow the motion of protein atoms over an enormous time range, from picoseconds to minutes (or longer), and with substantial structural specificity.
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Affiliation(s)
- Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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18
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Sakakura M, Morishima I, Terazima M. The Structural Dynamics and Ligand Releasing Process after the Photodissociation of Sperm Whale Carboxymyoglobin. J Phys Chem B 2001. [DOI: 10.1021/jp0116252] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masaki Sakakura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, and Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan
| | - Isao Morishima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, and Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, and Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan
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19
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Nishioku Y, Nakagawa M, Tsuda M, Terazima M. A spectrally silent transformation in the photolysis of octopus rhodopsin: a protein conformational change without any accompanying change of the chromophore's absorption. Biophys J 2001; 80:2922-7. [PMID: 11371464 PMCID: PMC1301475 DOI: 10.1016/s0006-3495(01)76257-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A spectrally silent transformation in the photolysis of octopus rhodopsin was detected by the time-resolved transient grating method. Our results showed that at least two photointermediates, which share the same chromophore absorption spectrum, exist after the final absorption changes. Previously, mesorhodopsin was thought to decay to the final photoproduct, acid metarhodopsin with a lifetime of 38 micros at 15 degrees C, but the present results show that there is at least one intermediate species (called transient acid metarhodopsin) with a lifetime of 180 micros at 15 degrees C, before forming acid metarhodopsin. This indicates that the parts of the protein distant from the chromophore are still changing even after the changes in microenvironment around the chromophore are over. From the signal intensity detected by the transient grating method, the volume change of the spectrally silent transformation was found to be DeltaV = 13 ml/mol. The activation energy of the spectrally silent transformation is much lower than those of other transformations of octopus rhodopsin. Since stable acid metarhodopsin has not been shown to activate the G protein, this transient acid metarhodopsin may be responsible for G protein activation.
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Affiliation(s)
- Y Nishioku
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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20
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Rosca F, Kumar ATN, Ionascu D, Sjodin T, Demidov AA, Champion PM. Wavelength selective modulation in femtosecond pump–probe spectroscopy and its application to heme proteins. J Chem Phys 2001. [DOI: 10.1063/1.1363673] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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21
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Barker BD, Larsen RW. Volume and enthalpy profiles of CO binding to Fe(II) tetrakis-(4-sulfonatophenyl)porphyrin. J Inorg Biochem 2001; 85:107-16. [PMID: 11410230 DOI: 10.1016/s0162-0134(01)00190-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The focus of this study is to examine volume and enthalpy profiles of ligand binding associated with CO-Fe(II) tetrakis-(4-sulfonato phenyl)-porphyrin (COFe(II)4SP) in aqueous solution. Temperature dependent photothermal beam deflection was employed to probe the overall enthalpy and volume changes associated with CO-photolysis and recombination. The analysis demonstrates that ligand recombination occurs with a pseudo first order rate constant of (2.5+/-0.2)x10(4) s(-1) (at 25 degrees C) with a corresponding volume decrease of 6+/-1 ml/mol. The activation enthalpy (DeltaH(double dagger)) and volume (DeltaV(double dagger)) change for CO recombination (determined from temperature/pressure dependent transient absorption spectroscopy) are found to be 3.9 kcal/mol and 8.2 ml/mol, respectively. These data are consistent with a mechanism in which photolysis yields a five-coordinate high spin (H(2)O)Fe(II)4SP complex that recombines in a single step to form the low spin (CO)(H(2)O)Fe(II)4SP complex. Base elimination, often associated with CO photolysis from hemes, is not observed in this system. The overall volume changes suggest a transition state with significant high spin character. Furthermore, these results demonstrate the utility of coupling photothermal techniques with variable pressure/temperature transient absorption spectroscopy to probe heme reaction dynamics.
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Affiliation(s)
- B D Barker
- Department of Chemistry, University of Hawaii-Manoa, 2545 the McCarthy Mall, Honolulu, HI 96822, USA
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22
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Dadusc G, Ogilvie JP, Schulenberg P, Marvet U, Miller RJ. Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: from "protein quakes" to ligand escape for myoglobin. Proc Natl Acad Sci U S A 2001; 98:6110-5. [PMID: 11344263 PMCID: PMC33430 DOI: 10.1073/pnas.101130298] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2000] [Accepted: 03/15/2001] [Indexed: 11/18/2022] Open
Abstract
Ligand transport through myoglobin (Mb) has been observed by using optically heterodyne-detected transient grating spectroscopy. Experimental implementation using diffractive optics has provided unprecedented sensitivity for the study of protein motions by enabling the passive phase locking of the four beams that constitute the experiment, and an unambiguous separation of the Real and Imaginary parts of the signal. Ligand photodissociation of carboxymyoglobin (MbCO) induces a sequence of events involving the relaxation of the protein structure to accommodate ligand escape. These motions show up in the Real part of the signal. The ligand (CO) transport process involves an initial, small amplitude, change in volume, reflecting the transit time of the ligand through the protein, followed by a significantly larger volume change with ligand escape to the surrounding water. The latter process is well described by a single exponential process of 725 +/- 15 ns. at room temperature. The overall dynamics provide a distinctive signature that can be understood in the context of segmental protein fluctuations that aid ligand escape via a few specific cavities, and they suggest the existence of discrete escape pathways.
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Affiliation(s)
- G Dadusc
- Department of Physics, University of Rochester, Rochester, NY 14627, USA
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23
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Sakakura M, Yamaguchi S, Hirota N, Terazima M. Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of carbon monoxide. J Am Chem Soc 2001; 123:4286-94. [PMID: 11457195 DOI: 10.1021/ja9944655] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The energetics and structural volume changes after photodissociation of carboxymyoglobin are quantitatively investigated by laser-induced transient grating (TG) and photoacoustic calorimetric techniques. Various origins of the TG signal are distinguished: the phase grating signals due to temperature change, due to absorption spectrum change, and due to volume change. We found a new kinetics of approximately 700 ns (at room temperature), which was not observed by the flash photolysis technique. This kinetics should be attributed to the intermediate between the geminate pair and the fully dissociated state. The enthalpy of an intermediate species is determined to be 61 +/- 10 kJ/mol, which is smaller than the expected Fe-CO bond energy. The volume of MbCO slightly contracts (5 +/- 3 cm(3)/mol) during this process. CO is fully released from the protein by an exponential kinetics from 25 to -2 degrees C. During this escaping process, the volume expands by 14.7 +/- 2 cm(3)/mol at room temperature and 14 +/- 10 kJ/mol is released, which should represent the protein relaxation and the solvation of the CO (the enthalpy of this final state is 47 +/- 10 kJ/mol). A potential barrier between the intermediate and the fully dissociated state is DeltaH(*) = 41.3 kJ/mol and DeltaS(*) = 13.6 J mol(-1) K(-1). The TG experiment under a high wavenumber reveals that the volume expansion depends on the temperature from 25 to -2 degrees C. The volume changes and the energies of the intermediate species are discussed.
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Affiliation(s)
- M Sakakura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606, Japan
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24
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Terazima M. Energy Transfer from Photoexcited Electronic States to the Thermal Modes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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25
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Rosca F, Kumar ATN, Ye X, Sjodin T, Demidov AA, Champion PM. Investigations of Coherent Vibrational Oscillations in Myoglobin. J Phys Chem A 2000. [DOI: 10.1021/jp993617f] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florin Rosca
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Anand T. N. Kumar
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Xiong Ye
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Theodore Sjodin
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Andrey A. Demidov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
| | - Paul M. Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115
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26
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Goodno GD, Astinov V, Miller RJD. Femtosecond Heterodyne-Detected Four-Wave-Mixing Studies of Deterministic Protein Motions. 2. Protein Response. J Phys Chem A 1999. [DOI: 10.1021/jp993559y] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gregory D. Goodno
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627
| | - Vladimir Astinov
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - R. J. Dwayne Miller
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario M5S 3H6 Canada
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27
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Barnes JP, Liang Z, Mchaourab HS, Freed JH, Hubbell WL. A multifrequency electron spin resonance study of T4 lysozyme dynamics. Biophys J 1999; 76:3298-306. [PMID: 10354455 PMCID: PMC1300299 DOI: 10.1016/s0006-3495(99)77482-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Electron spin resonance (ESR) spectroscopy at 250 GHz and 9 GHz is utilized to study the dynamics and local structural ordering of a nitroxide-labeled enzyme, T4 lysozyme (EC 3.2.1.17), in aqueous solution from 10 degrees C to 35 degrees C. Two separate derivatives, labeled at sites 44 and 69, were analyzed. The 250-GHz ESR spectra are well described by a microscopic ordering with macroscopic disordering (MOMD) model, which includes the influence of the tether connecting the probe to the protein. In the faster "time scale" of the 250-GHz ESR experiment, the overall rotational diffusion rate of the enzyme is too slow to significantly affect the spectrum, whereas for the 9-GHz ESR spectra, the overall rotational diffusion must be accounted for in the analysis. This is accomplished by using a slowly relaxing local structure model (SRLS) for the dynamics, wherein the tether motion and the overall motion are both included. In this way a simultaneous fit is successfully obtained for both the 250-GHz and 9-GHz ESR spectra. Two distinct motional/ordering modes of the probe are found for both lysozyme derivatives, indicating that the tether exists in two distinct conformations on the ESR time scale. The probe diffuses more rapidly about an axis perpendicular to its tether, which may result from fluctuations of the peptide backbone at the point of attachment of the spin probe.
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Affiliation(s)
- J P Barnes
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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28
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Callender RH, Dyer RB, Gilmanshin R, Woodruff WH. Fast events in protein folding: the time evolution of primary processes. Annu Rev Phys Chem 1999; 49:173-202. [PMID: 9933907 DOI: 10.1146/annurev.physchem.49.1.173] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most experimental studies on the dynamics of protein folding have been confined to timescales of 1 ms and longer. Yet it is obvious that many phenomena that are obligatory elements of the folding process occur on much faster timescales. For example, it is also now clear that the formation of secondary and tertiary structures can occur on nanosecond and microsecond times, respectively. Although fast events are essential to, and sometimes dominate, the overall folding process, with a few exceptions their experimental study has become possible only recently with the development of appropriate techniques. This review discusses new approaches that are capable of initiating and monitoring the fast events in protein folding with temporal resolution down to picoseconds. The first important results from those techniques, which have been obtained for the folding of some globular proteins and polypeptide models, are also discussed.
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Affiliation(s)
- R H Callender
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA. ,
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29
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Dyer RB, Gai F, Woodruff WH, Gilmanshin R, Callender RH. Infrared Studies of Fast Events in Protein Folding. Acc Chem Res 1998. [DOI: 10.1021/ar970343a] [Citation(s) in RCA: 157] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Deàk J, Chiu HL, Lewis CM, Miller RJD. Ultrafast Phase Grating Studies of Heme Proteins: Observation of the Low-Frequency Modes Directing Functionally Important Protein Motions. J Phys Chem B 1998. [DOI: 10.1021/jp980492q] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John Deàk
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario, M5S-1A1 Canada
| | - Hui-Ling Chiu
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario, M5S-1A1 Canada
| | - Caroline M. Lewis
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario, M5S-1A1 Canada
| | - R. J. Dwayne Miller
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario, M5S-1A1 Canada
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31
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Application of the transient grating technique to the study of the energetics and dynamics of electron transfer reactions: separation of an ion pair into free ions. J Photochem Photobiol A Chem 1998. [DOI: 10.1016/s1010-6030(97)00283-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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van Aalten DM, Conn DA, de Groot BL, Berendsen HJ, Findlay JB, Amadei A. Protein dynamics derived from clusters of crystal structures. Biophys J 1997; 73:2891-6. [PMID: 9414203 PMCID: PMC1181194 DOI: 10.1016/s0006-3495(97)78317-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins.
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Affiliation(s)
- D M van Aalten
- Department of Biochemistry and Molecular Biology, University of Leeds, England.
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33
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Affiliation(s)
- Gustavo A. Arteca
- Département de Chimie et Biochimie, Laurentian University, Ramsey Lake Road, Sudbury, Ontario, Canada P3E 2C6
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34
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On the time resolution of picosecond phase grating spectroscopy in tracing structural relaxation dynamics. Chem Phys Lett 1996. [DOI: 10.1016/0009-2614(96)00074-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Chen E, Kliger DS. Time-resolved near UV circular dichroism and absorption studies of carbonmonoxymyoglobin photolysis intermediates. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(95)04860-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Terazima M, Hara T, Hirota N. Reaction volume and enthalpy changes in photochemical reaction detected by the transient grating method; photodissociation of diphenylcyclopropenone. Chem Phys Lett 1995. [DOI: 10.1016/0009-2614(95)01164-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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37
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Ansari A, Jones CM, Henry ER, Hofrichter J, Eaton WA. Conformational relaxation and ligand binding in myoglobin. Biochemistry 1994; 33:5128-45. [PMID: 8172888 DOI: 10.1021/bi00183a017] [Citation(s) in RCA: 166] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Absorption spectroscopy with nanosecond time resolution shows that myoglobin undergoes conformational relaxation on the same time scale as geminate rebinding of carbon monoxide. Ligand rebinding following photodissociation of the heme-CO complex was measured from the amplitude of the average difference spectrum, while conformational changes were measured from changes in the detailed shape of the Soret spectra of the deoxyhemes. Experiments in which the solvent viscosity was varied between 1 and 300 cP and the temperature between 268 and 308 K were analyzed by fitting the multiwavelength kinetic data with both empirical and molecular models. Novel numerical techniques were employed in fitting the data, including the use of singular value decomposition to remove the effects of temperature and solvent on the spectra and of a Monte Carlo method to overcome the multiple minimum problem in searching parameter space. The molecular model is the minimal model that incorporates all of the major features of myoglobin kinetics at ambient temperatures, including a fast and slow rebinding conformation and two geminate states for each conformation. The results of fitting the kinetic data with this model indicate that the geminate-rebinding rates for the two conformations differ by at least a factor of 100. The differences between the spectra of the two conformations generated from the fits are similar to the differences between those of the R and T conformations of hemoglobin. In modeling the data, the dependence of the rates on temperature and viscosity was parametrized using a modification of Kramers theory which includes the contributions of both protein and solvent to the friction. The rate of the transition from the fast to the slow rebinding conformation is found to be inversely proportional to the viscosity when the viscosity exceeds about 30 cP and nearly viscosity independent at low viscosity. The viscosity dependence at high viscosities suggests that the two conformations differ by the global displacement of protein atoms on the proximal side of the heme observed by X-ray crystallography. We suggest that the conformational change observed in our experiments corresponds to the final portion of the nonexponential conformational relaxation recently observed by Anfinrud and co-workers, which begins on a picosecond time scale. Furthermore, extrapolation of our data to temperatures near that of the solvent glass transition suggests that this conformational relaxation may very well be the one postulated by Frauenfelder and co-workers to explain the decrease in the rate of geminate rebinding with increasing temperature above 180 K.
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Affiliation(s)
- A Ansari
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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38
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Lounnas V, Pettitt BM. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment. Proteins 1994; 18:133-47. [PMID: 8159663 DOI: 10.1002/prot.340180206] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
An analysis of a molecular dynamics simulation of metmyoglobin in an explicit solvent environment of 3,128 water molecules has been performed. Both statics and dynamics of the protein-solvent interface are addressed in a comparison with experiment. Three-dimensional density distributions, temperature factors, and occupancy weights are computed for the solvent by using the trajectory coordinates. Analysis of the hydration leads to the localization of more than 500 hydration sites distributed into multiple layers of solvation located between 2.6 and 6.8 A from the atomic protein surface. After locating the local solvent density maxima or hydration sites we conclude that water molecules of hydration positions and hydration sites are distinct concepts. Both global and detailed properties of the hydration cluster around myoglobin are compared with recent neutron and X-ray data on myoglobin. Questions arising from differences between X-ray and neutron data concerning the locations of the protein-bound water are investigated. Analysis of water site differences found from X-ray and neutron experiments compared with our simulation shows that the simulation gives a way to unify the hydration picture given by the two experiments.
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Affiliation(s)
- V Lounnas
- Department of Chemistry, University of Houston, Texas 77204-5641
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39
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Norris CL, Peters KS. A photoacoustic calorimetry study of horse carboxymyoglobin on the 10-nanosecond time scale. Biophys J 1993; 65:1660-5. [PMID: 8274654 PMCID: PMC1225892 DOI: 10.1016/s0006-3495(93)81223-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The development of a photoacoustic calorimeter with a time resolution of 10 ns is presented, and the dynamics of the enthalpy and volume changes found in the photodissociation of CO from horse carboxymyoglobin are examined. With this enhanced time resolution a new transient species, the lifetime of which is 29 ns at 20 degrees C, is observed in the ligand dissociation process.
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Affiliation(s)
- C L Norris
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215
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