A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins
Abstract
The mer operon in bacteria encodes a set of proteins and enzymes that impart resistance to environmental mercury toxicity by importing Hg2+ and reducing it to volatile Hg(0). Because the reduction occurs in the cytoplasm, mercuric ions must first be transported across the cytoplasmic membrane by one of a few known transporters. MerF is the smallest of these, containing only two transmembrane helices and two pairs of vicinal cysteines that coordinate mercuric ions. In this work, we use molecular dynamics simulations to characterize the dynamics of MerF in its apo and Hg2+-bound states. We find that the apo state positions one of the cysteine pairs closer to the periplasmic side of the membrane, while in the bound state the same pair approaches the cytoplasmic side. This finding is consistent with the functional requirement of accepting Hg2+ from the periplasmic space, sequestering it on acceptance, and transferring it to the cytoplasm. Conformational changes in the TM helices facilitate the functional interaction of the two cysteine pairs. Free-energy calculations provide a barrier of 16 kcal/mol for the association of the periplasmic Hg2+-bound protein MerP with MerF and 7 kcal/mol for the subsequent association of MerF's two cysteine pairs. Despite the significant conformationalmore »
- Authors:
-
- Georgia Inst. of Technology, Atlanta, GA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Georgia Inst. of Technology, Atlanta, GA (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)
- OSTI Identifier:
- 1607025
- Alternate Identifier(s):
- OSTI ID: 1574067
- Grant/Contract Number:
- AC05-00OR22725; SC0014664; R01-GM123169; OCI-1053575
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Computational Chemistry
- Additional Journal Information:
- Journal Volume: 41; Journal Issue: 6; Journal ID: ISSN 0192-8651
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; MerF; mercury transport; membrane transporter; free-energy calculations; molecular dynamics
Citation Formats
Hwang, Hyea J., Hazel, Anthony, Lian, Peng, Smith, Jeremy C., Gumbart, James C., and Parks, Jerry M. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. United States: N. p., 2019.
Web. doi:10.1002/jcc.26098.
Hwang, Hyea J., Hazel, Anthony, Lian, Peng, Smith, Jeremy C., Gumbart, James C., & Parks, Jerry M. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. United States. https://doi.org/10.1002/jcc.26098
Hwang, Hyea J., Hazel, Anthony, Lian, Peng, Smith, Jeremy C., Gumbart, James C., and Parks, Jerry M. Wed .
"A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins". United States. https://doi.org/10.1002/jcc.26098. https://www.osti.gov/servlets/purl/1607025.
@article{osti_1607025,
title = {A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins},
author = {Hwang, Hyea J. and Hazel, Anthony and Lian, Peng and Smith, Jeremy C. and Gumbart, James C. and Parks, Jerry M.},
abstractNote = {The mer operon in bacteria encodes a set of proteins and enzymes that impart resistance to environmental mercury toxicity by importing Hg2+ and reducing it to volatile Hg(0). Because the reduction occurs in the cytoplasm, mercuric ions must first be transported across the cytoplasmic membrane by one of a few known transporters. MerF is the smallest of these, containing only two transmembrane helices and two pairs of vicinal cysteines that coordinate mercuric ions. In this work, we use molecular dynamics simulations to characterize the dynamics of MerF in its apo and Hg2+-bound states. We find that the apo state positions one of the cysteine pairs closer to the periplasmic side of the membrane, while in the bound state the same pair approaches the cytoplasmic side. This finding is consistent with the functional requirement of accepting Hg2+ from the periplasmic space, sequestering it on acceptance, and transferring it to the cytoplasm. Conformational changes in the TM helices facilitate the functional interaction of the two cysteine pairs. Free-energy calculations provide a barrier of 16 kcal/mol for the association of the periplasmic Hg2+-bound protein MerP with MerF and 7 kcal/mol for the subsequent association of MerF's two cysteine pairs. Despite the significant conformational changes required to move the binding site across the membrane, coarse-grained simulations of multiple copies of MerF support the expectation that it functions as a monomer. Finally, our results demonstrate how conformational changes and binding thermodynamics could lead to such a small membrane protein acting as an ion transporter.},
doi = {10.1002/jcc.26098},
journal = {Journal of Computational Chemistry},
number = 6,
volume = 41,
place = {United States},
year = {Wed Nov 13 00:00:00 EST 2019},
month = {Wed Nov 13 00:00:00 EST 2019}
}
Web of Science
Works referenced in this record:
Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method
journal, March 2018
- Gumbart, James C.; Ulmschneider, Martin B.; Hazel, Anthony
- The Journal of Membrane Biology, Vol. 251, Issue 3
MerF is a mercury transport protein: different structures but a common mechanism for mercuric ion transporters?
journal, April 2000
- Wilson, Jon R.; Leang, Ching; Morby, Andrew P.
- FEBS Letters, Vol. 472, Issue 1
The ORCA program system: The ORCA program system
journal, June 2011
- Neese, Frank
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 1
Hypersensitivity to Hg2+ and hyperbinding activity associated with cloned fragments of the mercurial resistance operon of plasmid NR1.
journal, January 1979
- Nakahara, H.; Silver, S.; Miki, T.
- Journal of Bacteriology, Vol. 140, Issue 1
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds
journal, March 2016
- Lee, Christopher T.; Comer, Jeffrey; Herndon, Conner
- Journal of Chemical Information and Modeling, Vol. 56, Issue 4
Role of MerC, MerE, MerF, MerT, and/or MerP in Resistance to Mercurials and the Transport of Mercurials in Escherichia coli
journal, January 2013
- Sone, Yuka; Nakamura, Ryosuke; Pan-Hou, Hidemitsu
- Biological and Pharmaceutical Bulletin, Vol. 36, Issue 11
Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace
journal, July 2016
- Zhang, Cheng; Lai, Chun-Liang; Pettitt, B. Montgomery
- Molecular Simulation, Vol. 42, Issue 13
Crystal Structure of the Oxidized Form of the Periplasmic Mercury-binding Protein MerP from Ralstonia metallidurans CH34
journal, May 2004
- Serre, Laurence; Rossy, Emmanuel; Pebay-Peyroula, Eva
- Journal of Molecular Biology, Vol. 339, Issue 1
Structure of the membrane protein MerF, a bacterial mercury transporter, improved by the inclusion of chemical shift anisotropy constraints
journal, August 2014
- Tian, Ye; Lu, George J.; Marassi, Francesca M.
- Journal of Biomolecular NMR, Vol. 60, Issue 1
Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems
journal, June 2014
- Moradi, Mahmoud; Tajkhorshid, Emad
- Journal of Chemical Theory and Computation, Vol. 10, Issue 7
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
Structure Determination of a Membrane Protein with Two Trans-membrane Helices in Aligned Phospholipid Bicelles by Solid-State NMR Spectroscopy
journal, September 2006
- De Angelis, Anna A.; Howell, Stanley C.; Nevzorov, Alexander A.
- Journal of the American Chemical Society, Vol. 128, Issue 37
Constant pressure molecular dynamics simulation: The Langevin piston method
journal, September 1995
- Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W.
- The Journal of Chemical Physics, Vol. 103, Issue 11
Rapid parameterization of small molecules using the force field toolkit
journal, September 2013
- Mayne, Christopher G.; Saam, Jan; Schulten, Klaus
- Journal of Computational Chemistry, Vol. 34, Issue 32
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
journal, November 2016
- Huang, Jing; Rauscher, Sarah; Nawrocki, Grzegorz
- Nature Methods, Vol. 14, Issue 1
The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology
journal, November 1986
- von Heijne, Gunnar
- The EMBO Journal, Vol. 5, Issue 11
NMR Solution Structure of the Oxidized Form of MerP, a Mercuric Ion Binding Protein Involved in Bacterial Mercuric Ion Resistance † , ‡
journal, June 1998
- Qian, Hong; Sahlman, Lena; Eriksson, Per-Olof
- Biochemistry, Vol. 37, Issue 26
All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms
journal, May 2008
- Pantazis, Dimitrios A.; Chen, Xian-Yang; Landis, Clark R.
- Journal of Chemical Theory and Computation, Vol. 4, Issue 6
Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain
journal, May 2012
- Pandit, Kunal R.; Klauda, Jeffery B.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 5
Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane
journal, August 2017
- Zhou, Jing; Smith, Micholas Dean; Cooper, Sarah J.
- Environmental Science & Technology, Vol. 51, Issue 18
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
journal, August 2014
- Comer, Jeffrey; Gumbart, James C.; Hénin, Jérôme
- The Journal of Physical Chemistry B, Vol. 119, Issue 3
Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993
- Becke, Axel D.
- The Journal of Chemical Physics, Vol. 98, Issue 7, p. 5648-5652
Mercuric ion-resistance operons of plasmid R100 and transposon Tn501: the beginning of the operon including the regulatory region and the first two structural genes.
journal, October 1984
- Misra, T. K.; Brown, N. L.; Fritzinger, D. C.
- Proceedings of the National Academy of Sciences, Vol. 81, Issue 19
NMR Structure Determination of a Membrane Protein with Two Transmembrane Helices in Micelles: MerF of the Bacterial Mercury Detoxification System † , ‡
journal, April 2005
- Howell, Stanley C.; Mesleh, Michael F.; Opella, Stanley J.
- Biochemistry, Vol. 44, Issue 13
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993
- Darden, Tom; York, Darrin; Pedersen, Lee
- The Journal of Chemical Physics, Vol. 98, Issue 12
Structure Determination of a Membrane Protein in Proteoliposomes
journal, January 2012
- Das, Bibhuti B.; Nothnagel, Henry J.; Lu, George J.
- Journal of the American Chemical Society, Vol. 134, Issue 4
The Structure of the Metal-Binding Motif GMTCAAC Is Similar in an 18-Residue Linear Peptide and the Mercury Binding Protein MerP
journal, March 2000
- Veglia, G.; Porcelli, F.; DeSilva, T.
- Journal of the American Chemical Society, Vol. 122, Issue 10
Role of the merT and merP gene products of transposon Tn501 in the induction and expression of resistance to mercuric ions
journal, January 1987
- Lund, Peter A.; Brown, Nigel L.
- Gene, Vol. 52, Issue 2-3
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012
- Best, Robert B.; Zhu, Xiao; Shim, Jihyun
- Journal of Chemical Theory and Computation, Vol. 8, Issue 9
New model potentials for sulfur–copper(I) and sulfur–mercury(II) interactions in proteins: Fromab initio to molecular dynamics
journal, January 2006
- Fuchs, Jean-Francois; Nedev, Hristo; Poger, David
- Journal of Computational Chemistry, Vol. 27, Issue 7
Multidimensional replica-exchange method for free-energy calculations
journal, October 2000
- Sugita, Yuji; Kitao, Akio; Okamoto, Yuko
- The Journal of Chemical Physics, Vol. 113, Issue 15
Microsecond Molecular Dynamics Simulations of Lipid Mixing
journal, September 2014
- Hong, Chunkit; Tieleman, D. Peter; Wang, Yi
- Langmuir, Vol. 30, Issue 40
Structures of the Reduced and Mercury-Bound Forms of MerP, the Periplasmic Protein from the Bacterial Mercury Detoxification System † , ‡
journal, June 1997
- Steele, Ruth A.; Opella, Stanley J.
- Biochemistry, Vol. 36, Issue 23
Bacterial mercury resistance from atoms to ecosystems
journal, June 2003
- Barkay, Tamar; Miller, Susan M.; Summers, Anne O.
- FEMS Microbiology Reviews, Vol. 27, Issue 2-3
Biophysical characterization of the MerP-like amino-terminal extension of the mercuric reductase from Ralstonia metallidurans CH34
journal, November 2003
- Rossy, Emmanuel; Champier, Ludovic; Bersch, Beate
- JBIC Journal of Biological Inorganic Chemistry, Vol. 9, Issue 1
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
journal, July 2007
- Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
- The Journal of Physical Chemistry B, Vol. 111, Issue 27
Folding free energy landscapes of β -sheets with non-polarizable and polarizable CHARMM force fields
journal, August 2018
- Hazel, Anthony J.; Walters, Evan T.; Rowley, Christopher N.
- The Journal of Chemical Physics, Vol. 149, Issue 7
X-ray Structure of a Hg 2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg 2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs
journal, November 2014
- Lian, Peng; Guo, Hao-Bo; Riccardi, Demian
- Biochemistry, Vol. 53, Issue 46
Energy-adjustedab initio pseudopotentials for the second and third row transition elements
journal, January 1990
- Andrae, D.; H�u�ermann, U.; Dolg, M.
- Theoretica Chimica Acta, Vol. 77, Issue 2
Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers
journal, October 2011
- Neale, Chris; Bennett, W. F. Drew; Tieleman, D. Peter
- Journal of Chemical Theory and Computation, Vol. 7, Issue 12
Distribution of mechanical stress in the Escherichia coli cell envelope
journal, December 2018
- Hwang, Hyea; Paracini, Nicolò; Parks, Jerry M.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1860, Issue 12
Decrypting protein insertion through the translocon with free-energy calculations
journal, July 2016
- Gumbart, James C.; Chipot, Christophe
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1858, Issue 7
Excessive aggregation of membrane proteins in the Martini model
journal, November 2017
- Javanainen, Matti; Martinez-Seara, Hector; Vattulainen, Ilpo
- PLOS ONE, Vol. 12, Issue 11
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
journal, November 1994
- Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.
- The Journal of Physical Chemistry, Vol. 98, Issue 45, p. 11623-11627
Molecular density functional calculations in the regular relativistic approximation: Method, application to coinage metal diatomics, hydrides, fluorides and chlorides, and comparison with first-order relativistic calculations
journal, July 1998
- van Wüllen, Christoph
- The Journal of Chemical Physics, Vol. 109, Issue 2
The Structure of the Mercury Transporter MerF in Phospholipid Bilayers: A Large Conformational Rearrangement Results from N-Terminal Truncation
journal, June 2013
- Lu, George J.; Tian, Ye; Vora, Nemil
- Journal of the American Chemical Society, Vol. 135, Issue 25
VMD: Visual molecular dynamics
journal, February 1996
- Humphrey, William; Dalke, Andrew; Schulten, Klaus
- Journal of Molecular Graphics, Vol. 14, Issue 1
Improving the specificity of organophosphorus hydrolase to acephate by mutagenesis at its binding site: a computational study
journal, May 2021
- Badakhshan, Reza; Mohammadi, Mozafar; Farnoosh, Gholamreza
- Journal of Molecular Modeling, Vol. 27, Issue 6
Distribution of Mechanical Stress in the Escherichia Coli Cell Envelope
journal, February 2019
- Hwang, Sunny; Paracini, Nicolo; Parks, Jerry M.
- Biophysical Journal, Vol. 116, Issue 3
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
text, January 1988
- Robert, Parr,; Chengteh, Lee,; Weitao, Yang,
- The University of North Carolina at Chapel Hill University Libraries
Multidimensional replica-exchange method for free-energy calculations
text, January 2000
- Sugita, Yuji; Kitao, Akio; Okamoto, Yuko
- arXiv