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Title: Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II

Abstract

The second-shell ammonia binding sites near the oxygen-evolving complex are characterized by Continuum Electrostatic/Monte Carlo (MCCE), QM/MM and DFT calculations and experimental measurements.

Authors:
 [1];  [2];  [2];  [3]; ORCiD logo [2];  [2];  [1]
  1. Department of Physics; City College of New York; C.U.N.Y. New York 10031; USA
  2. Department of Chemistry; Yale University; New Haven; USA
  3. Center for Free-Electron Laser Science (CFEL); Deutsches Elektronen-Synchrotron DESY; 22607 Hamburg; Germany
Publication Date:
Research Org.:
Yale Univ., New Haven, CT (United States); City Univ. of New York (CUNY), NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1539918
DOE Contract Number:  
FG02-05ER15646; SC0001423
Resource Type:
Journal Article
Journal Name:
Dalton Transactions
Additional Journal Information:
Journal Volume: 46; Journal Issue: 46; Journal ID: ISSN 1477-9226
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
Chemistry

Citation Formats

Mandal, Manoj, Askerka, Mikhail, Banerjee, Gourab, Amin, Muhammed, Brudvig, Gary W., Batista, Victor S., and Gunner, M. R. Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II. United States: N. p., 2017. Web. doi:10.1039/c7dt03901h.
Mandal, Manoj, Askerka, Mikhail, Banerjee, Gourab, Amin, Muhammed, Brudvig, Gary W., Batista, Victor S., & Gunner, M. R. Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II. United States. doi:10.1039/c7dt03901h.
Mandal, Manoj, Askerka, Mikhail, Banerjee, Gourab, Amin, Muhammed, Brudvig, Gary W., Batista, Victor S., and Gunner, M. R. Sun . "Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II". United States. doi:10.1039/c7dt03901h.
@article{osti_1539918,
title = {Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II},
author = {Mandal, Manoj and Askerka, Mikhail and Banerjee, Gourab and Amin, Muhammed and Brudvig, Gary W. and Batista, Victor S. and Gunner, M. R.},
abstractNote = {The second-shell ammonia binding sites near the oxygen-evolving complex are characterized by Continuum Electrostatic/Monte Carlo (MCCE), QM/MM and DFT calculations and experimental measurements.},
doi = {10.1039/c7dt03901h},
journal = {Dalton Transactions},
issn = {1477-9226},
number = 46,
volume = 46,
place = {United States},
year = {2017},
month = {1}
}

Works referenced in this record:

Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å
journal, April 2011

  • Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren
  • Nature, Vol. 473, Issue 7345
  • DOI: 10.1038/nature09913

COOPERATION OF CHARGES IN PHOTOSYNTHETIC O 2 EVOLUTION–I. A LINEAR FOUR STEP MECHANISM
journal, June 1970


Water-Splitting Chemistry of Photosystem II
journal, November 2006

  • McEvoy, James P.; Brudvig, Gary W.
  • Chemical Reviews, Vol. 106, Issue 11
  • DOI: 10.1021/cr0204294

Biological Water Oxidation
journal, March 2013

  • Cox, Nicholas; Pantazis, Dimitrios A.; Neese, Frank
  • Accounts of Chemical Research, Vol. 46, Issue 7
  • DOI: 10.1021/ar3003249

The Structure of Photosystem II and the Mechanism of Water Oxidation in Photosynthesis
journal, April 2015


OO Bond Formation in the S4 State of the Oxygen-Evolving Complex in Photosystem II
journal, December 2006


NH 3 Binding to the S 2 State of the O 2 -Evolving Complex of Photosystem II: Analogue to H 2 O Binding during the S 2 → S 3 Transition
journal, September 2015


Progress Toward a Molecular Mechanism of Water Oxidation in Photosystem II
journal, May 2017


A five-coordinate Mn( iv ) intermediate in biological water oxidation: spectroscopic signature and a pivot mechanism for water binding
journal, January 2016

  • Retegan, Marius; Krewald, Vera; Mamedov, Fikret
  • Chemical Science, Vol. 7, Issue 1
  • DOI: 10.1039/C5SC03124A

A proposal for water oxidation in photosystem II
journal, January 1998

  • Pecoraro, V. L.; Baldwin, M. J.; Caudle, M. T.
  • Pure and Applied Chemistry, Vol. 70, Issue 4
  • DOI: 10.1351/pac199870040925

Water oxidation chemistry of photosystem II
journal, October 2007

  • Brudvig, Gary W.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, Issue 1494
  • DOI: 10.1098/rstb.2007.2217

The chloride requirement for photosynthetic oxygen evolution. Analysis of the effects of chloride and other anions on amine inhibition of the oxygen-evolving complex
journal, September 1984

  • Sandusky, Peter O.; Yocum, Charles F.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 766, Issue 3
  • DOI: 10.1016/0005-2728(84)90121-X

Binding of amines to the oxygen-evolving center of photosystem II
journal, October 1986


Ammonia binding to the oxygen-evolving complex of photosystem II identifies the solvent-exchangeable oxygen bridge ( -oxo) of the manganese tetramer
journal, September 2013

  • Perez Navarro, M.; Ames, W. M.; Nilsson, H.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 39
  • DOI: 10.1073/pnas.1304334110

Ammonia Binds to the Dangler Manganese of the Photosystem II Oxygen-Evolving Complex
journal, July 2015

  • Oyala, Paul H.; Stich, Troy A.; Debus, Richard J.
  • Journal of the American Chemical Society, Vol. 137, Issue 27
  • DOI: 10.1021/jacs.5b04768

Interaction and Inhibitory Effect of Ammonium Cation in the Oxygen Evolving Center of Photosytem II
journal, April 2011

  • Tsuno, Masaya; Suzuki, Hiroyuki; Kondo, Toru
  • Biochemistry, Vol. 50, Issue 13
  • DOI: 10.1021/bi101952g

The chloride requirement for photosynthetic oxygen evolution: Factors affecting nucleophilic displacement of chloride from the oxygen-evolving complex
journal, April 1986


Ammonia Binding in the Second Coordination Sphere of the Oxygen-Evolving Complex of Photosystem II
journal, July 2016


The calcium and chloride requirements of the O2 evolving complex
journal, February 2008


Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride
journal, February 2009

  • Guskov, Albert; Kern, Jan; Gabdulkhakov, Azat
  • Nature Structural & Molecular Biology, Vol. 16, Issue 3
  • DOI: 10.1038/nsmb.1559

Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography
journal, May 2009

  • Kawakami, K.; Umena, Y.; Kamiya, N.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 21
  • DOI: 10.1073/pnas.0812797106

Chloride Regulation of Enzyme Turnover: Application to the Role of Chloride in Photosystem II
journal, April 2011

  • Pokhrel, Ravi; McConnell, Iain L.; Brudvig, Gary W.
  • Biochemistry, Vol. 50, Issue 14
  • DOI: 10.1021/bi2000388

Photosystem II, the water-splitting enzyme
journal, June 1989


Structural–Functional Role of Chloride in Photosystem II
journal, July 2011

  • Rivalta, Ivan; Amin, Muhamed; Luber, Sandra
  • Biochemistry, Vol. 50, Issue 29
  • DOI: 10.1021/bi200685w

Effect of Chloride Depletion on the Magnetic Properties and the Redox Leveling of the Oxygen-Evolving Complex in Photosystem II
journal, April 2016

  • Amin, Muhamed; Pokhrel, Ravi; Brudvig, Gary W.
  • The Journal of Physical Chemistry B, Vol. 120, Issue 18
  • DOI: 10.1021/acs.jpcb.6b03545

Mutation of Lysine 317 in the D2 Subunit of Photosystem II Alters Chloride Binding and Proton Transport
journal, July 2013

  • Pokhrel, Ravi; Service, Rachel J.; Debus, Richard J.
  • Biochemistry, Vol. 52, Issue 28
  • DOI: 10.1021/bi301700u

Two Interconvertible Structures that Explain the Spectroscopic Properties of the Oxygen-Evolving Complex of Photosystem II in the S 2 State
journal, August 2012

  • Pantazis, Dimitrios A.; Ames, William; Cox, Nicholas
  • Angewandte Chemie International Edition, Vol. 51, Issue 39
  • DOI: 10.1002/anie.201204705

Properties of the Chloride-Depleted Oxygen-Evolving Complex of Photosystem II Studied by Electron Paramagnetic Resonance
journal, January 1996

  • van Vliet, Pieter; Rutherford, A. William
  • Biochemistry, Vol. 35, Issue 6
  • DOI: 10.1021/bi9514471

EPR evidence for a modified S-state transition in chloride-depleted Photosystem II
journal, September 1986

  • Ono, T.; Zimmermann, J. L.; Inoue, Y.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 851, Issue 2
  • DOI: 10.1016/0005-2728(86)90125-8

Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II
journal, December 2014

  • Amin, Muhamed; Vogt, Leslie; Szejgis, Witold
  • The Journal of Physical Chemistry B, Vol. 119, Issue 24
  • DOI: 10.1021/jp510948e

Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory
journal, December 1994

  • Tannor, David J.; Marten, Bryan; Murphy, Robert
  • Journal of the American Chemical Society, Vol. 116, Issue 26
  • DOI: 10.1021/ja00105a030

Calculation of Proton Transfers in Bacteriorhodopsin bR and M Intermediates
journal, August 2003

  • Song, Yifan; Mao, Junjun; Gunner, M. R.
  • Biochemistry, Vol. 42, Issue 33
  • DOI: 10.1021/bi034482d

Using Multiconformation Continuum Electrostatics to Compare Chloride Binding Motifs in α-Amylase, Human Serum Albumin, and Omp32
journal, April 2009


S 0 -State Model of the Oxygen-Evolving Complex of Photosystem II
journal, October 2013

  • Pal, Rhitankar; Negre, Christian F. A.; Vogt, Leslie
  • Biochemistry, Vol. 52, Issue 44
  • DOI: 10.1021/bi401214v

Structural Changes in the Oxygen-Evolving Complex of Photosystem II Induced by the S 1 to S 2 Transition: A Combined XRD and QM/MM Study
journal, October 2014

  • Askerka, Mikhail; Wang, Jimin; Brudvig, Gary W.
  • Biochemistry, Vol. 53, Issue 44
  • DOI: 10.1021/bi5011915

A highly resolved, oxygen-evolving photosystem II preparation from spinach thylakoid membranes: EPR and electron-transport properties
journal, November 1981


Active and resting states of the oxygen-evolving complex of photosystem II
journal, June 1985

  • Beck, Warren F.; De Paula, Julio C.; Brudvig, Gary W.
  • Biochemistry, Vol. 24, Issue 12
  • DOI: 10.1021/bi00333a035

Oxygen-Evolving Mn Cluster in Photosystem II: The Protonation Pattern and Oxidation State in the High-Resolution Crystal Structure
journal, April 2012

  • Galstyan, Artur; Robertazzi, Arturo; Knapp, Ernst Walter
  • Journal of the American Chemical Society, Vol. 134, Issue 17
  • DOI: 10.1021/ja300254n

Water oxidation energy diagrams for photosystem II for different protonation states, and the effect of removing calcium
journal, January 2014

  • Siegbahn, Per E. M.
  • Physical Chemistry Chemical Physics, Vol. 16, Issue 24
  • DOI: 10.1039/c3cp55329a

Theoretical studies of the damage-free S1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II
journal, March 2015


Redox-coupled substrate water reorganization in the active site of Photosystem II—The role of calcium in substrate water delivery
journal, June 2016

  • Ugur, Ilke; Rutherford, A. William; Kaila, Ville R. I.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1857, Issue 6
  • DOI: 10.1016/j.bbabio.2016.01.015

Analysis of the Radiation-Damage-Free X-ray Structure of Photosystem II in Light of EXAFS and QM/MM Data
journal, February 2015


Energetics of the S 2 State Spin Isomers of the Oxygen-Evolving Complex of Photosystem II
journal, January 2017

  • Vinyard, David J.; Khan, Sahr; Askerka, Mikhail
  • The Journal of Physical Chemistry B, Vol. 121, Issue 5
  • DOI: 10.1021/acs.jpcb.7b00110

EPR Study of the Oxygen Evolving Complex in His-Tagged Photosystem II from the Cyanobacterium Synechococcus elongatus
journal, November 2000

  • Boussac, Alain; Sugiura, Miwa; Inoue, Yorinao
  • Biochemistry, Vol. 39, Issue 45
  • DOI: 10.1021/bi001159r

The g = 4.1 EPR signal of the S2 state of the photosynthetic oxygen-evolving complex arises from a multinuclear manganese cluster
journal, December 1990

  • Kim, Dennis H.; Britt, R. David; Klein, Melvin P.
  • Journal of the American Chemical Society, Vol. 112, Issue 25
  • DOI: 10.1021/ja00181a049

Tracking the Flow of Water through Photosystem II Using Molecular Dynamics and Streamline Tracing
journal, March 2010

  • Vassiliev, Serguei; Comte, Pascal; Mahboob, Abdullah
  • Biochemistry, Vol. 49, Issue 9
  • DOI: 10.1021/bi901900s