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Title: Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering

Abstract

Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find thatmore » the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1]
  1. KAIST, Daejeon (South Korea); Inst. for Basic Science (IBS), Daejeon (South Korea)
  2. Inha Univ., Incheon (South Korea)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Research Foundation of Korea (NRF); NIH National Inst. of General Medical Sciences
OSTI Identifier:
1248391
Grant/Contract Number:  
AC02-06CH11357; NRF-2014R1A1A1002511; R24GM111072
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Structural Dynamics
Additional Journal Information:
Journal Volume: 3; Journal Issue: 2; Journal ID: ISSN 2329-7778
Publisher:
American Crystallographic Association/AIP
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Kim, Jong Goo, Muniyappan, Srinivasan, Oang, Key Young, Kim, Tae Wu, Yang, Cheolhee, Kim, Kyung Hwan, Kim, Jeongho, and Ihee, Hyotcherl. Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering. United States: N. p., 2016. Web. doi:10.1063/1.4947071.
Kim, Jong Goo, Muniyappan, Srinivasan, Oang, Key Young, Kim, Tae Wu, Yang, Cheolhee, Kim, Kyung Hwan, Kim, Jeongho, & Ihee, Hyotcherl. Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering. United States. https://doi.org/10.1063/1.4947071
Kim, Jong Goo, Muniyappan, Srinivasan, Oang, Key Young, Kim, Tae Wu, Yang, Cheolhee, Kim, Kyung Hwan, Kim, Jeongho, and Ihee, Hyotcherl. 2016. "Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering". United States. https://doi.org/10.1063/1.4947071. https://www.osti.gov/servlets/purl/1248391.
@article{osti_1248391,
title = {Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering},
author = {Kim, Jong Goo and Muniyappan, Srinivasan and Oang, Key Young and Kim, Tae Wu and Yang, Cheolhee and Kim, Kyung Hwan and Kim, Jeongho and Ihee, Hyotcherl},
abstractNote = {Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.},
doi = {10.1063/1.4947071},
url = {https://www.osti.gov/biblio/1248391}, journal = {Structural Dynamics},
issn = {2329-7778},
number = 2,
volume = 3,
place = {United States},
year = {Thu Apr 14 00:00:00 EDT 2016},
month = {Thu Apr 14 00:00:00 EDT 2016}
}

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Cited by: 18 works
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Works referenced in this record:

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Solvent dependent structural perturbations of chemical reaction intermediates visualized by time-resolved x-ray diffraction
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Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering
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Mutational destabilization of the critical interface water cluster in Scapharca dimeric hemoglobin: structural basis for altered allosteric activity
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Time-Resolved Small-Angle X-ray Scattering Study of the Folding Dynamics of Barnase
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Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump–Probe X-ray Solution Scattering
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Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
journal, August 2014


Direct observation of bond formation in solution with femtosecond X-ray scattering
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Visualizing Chemical Reactions in Solution by Picosecond X-Ray Diffraction
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Insight into the Allosteric Mechanism of Scapharca Dimeric Hemoglobin
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Cooperative Oxygen Binding to Scapharca inaequivalvis Hemoglobin in the Crystal
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Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser
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Unveiling the Timescale of the R–T Transition in Human Hemoglobin
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Rotational dephasing of a gold complex probed by anisotropic femtosecond x-ray solution scattering using an x-ray free-electron laser
journal, November 2015


Direct observation of photolysis-induced tertiary structural changes in hemoglobin
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Residue F4 Plays a Key Role in Modulating Oxygen Affinity and Cooperativity in Scapharca Dimeric Hemoglobin
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Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering
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Protein Tertiary Structural Changes Visualized by Time-Resolved X-ray Solution Scattering
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An Optical Signal Correlated with the Allosteric Transition in Scapharca inaequivalvis HbI
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The Apolar Distal Histidine Mutant (His69→Val) of the Homodimeric Scapharca Hemoglobin Is in an R -like Conformation
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Mutational destabilization of the critical interface water cluster in Scapharca dimeric hemoglobin: structural basis for altered allosteric activity
journal, December 1998


Haemoglobin: The structural changes related to ligand binding and its allosteric mechanism
journal, April 1979


The crystal structure of human deoxyhaemoglobin at 1.74 Å resolution
journal, May 1984


Structural Dynamics of Light-Driven Proton Pumps
journal, January 2010


Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin
journal, September 2011


Unveiling the Timescale of the R–T Transition in Human Hemoglobin
journal, July 2010


Kinetics of ligand binding and quaternary conformational change in the homodimeric hemoglobin from Scapharca inaequivalvis.
journal, June 1984


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journal, November 1983


Visualizing Solution-Phase Reaction Dynamics with Time-Resolved X-ray Liquidography
journal, February 2009


An Optical Signal Correlated with the Allosteric Transition in Scapharca inaequivalvis HbI
journal, December 2006


Insight into the Allosteric Mechanism of Scapharca Dimeric Hemoglobin
journal, November 2014


The Apolar Distal Histidine Mutant (His69→Val) of the Homodimeric Scapharca Hemoglobin Is in an R -like Conformation
journal, April 1998


Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering
journal, February 2012


Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump–Probe X-ray Solution Scattering
journal, April 2012


Direct observation of bond formation in solution with femtosecond X-ray scattering
journal, February 2015


Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering
journal, September 2008


Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
journal, August 2014


Solvent dependent structural perturbations of chemical reaction intermediates visualized by time-resolved x-ray diffraction
journal, April 2009


Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins
journal, August 2011


Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin
journal, May 2006


Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering
journal, April 2010


Direct observation of photolysis-induced tertiary structural changes in hemoglobin
journal, May 2003


Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin
journal, December 1996


Cooperative Oxygen Binding to Scapharca inaequivalvis Hemoglobin in the Crystal
journal, February 1996


Bacterial Expression Of Scapharca Dimeric Hemoglobin: A Simple Model System For Investigating Protein Cooperativity
journal, January 1995


Hemoglobin allostery: resonance Raman spectroscopy of kinetic intermediates
journal, September 1995


Works referencing / citing this record:

Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering
journal, November 2018


Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme
journal, September 2019


Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme
journal, September 2019


Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering
journal, November 2018