1
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Ranepura GA, Mao J, Vermaas JV, Wang J, Gisriel CJ, Wei RJ, Ortiz-Soto J, Uddin MR, Amin M, Brudvig GW, Gunner MR. Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II. J Phys Chem B 2023; 127:10974-10986. [PMID: 38097367 DOI: 10.1021/acs.jpcb.3c06273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment-protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (-CH3) on one of its pyrrole rings, while Chl b has a formyl group (-CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a. It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type (a or b) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b. The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a-binding sites. It is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.
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Affiliation(s)
- Gehan A Ranepura
- Ph.D. Program in Physics, The Graduate Center, City University of New York, New York, New York 10016, United States
- Department of Physics, City College of New York, New York, New York 10031, United States
| | - Junjun Mao
- Benjamin Levich Institute for Physico-Chemical Hydrodynamics, City College of New York, New York, New York 10031, United States
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, Michigan 48824, United States
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Christopher J Gisriel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Rongmei Judy Wei
- Department of Physics, City College of New York, New York, New York 10031, United States
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - Jose Ortiz-Soto
- Department of Physics, City College of New York, New York, New York 10031, United States
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - Md Raihan Uddin
- Department of Physics, City College of New York, New York, New York 10031, United States
- Ph.D. Program in Biochemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - Muhamed Amin
- Laboratory of Computational Biology, National Heart, Lung and Blood, Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - M R Gunner
- PhD Program in Physics, in Chemistry and in Biochemistry at the Graduate Center, City University of New York, New York, New York 10016, United States
- Department of Physics, City College of New York, New York, New York 10031, United States
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2
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da Rocha L, Baptista AM, Campos SRR. Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin. J Phys Chem B 2022; 126:9123-9136. [PMID: 36321840 PMCID: PMC9776516 DOI: 10.1021/acs.jpcb.2c03797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ions are involved in multiple biological processes and may exist bound to biomolecules or may be associated with their surface. Although the presence of ions in nucleic acids has traditionally gained more interest, ion-protein interactions, often with a marked dependency on pH, are beginning to gather attention. Here we present a detailed analysis on the binding and distribution of ions around β-lactoglobulin using a constant-pH MD (CpHMD) method, at a pH range 3-8, and compare it with the more traditional Poisson-Boltzmann (PB) model and the existing experimental data. Most analyses used ion concentration maps built around the protein, obtained from either the CpHMD simulations or PB calculations. The requirements of approximate charge neutrality and ionic strength equal to bulk, imposed on the MD box, imply that the absolute value of the ion excess should be half the protein charge, which is in agreement with experimental observation on other proteins ( Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2015879118) and lends support to this protocol. In addition, the protein total charge (including territorially bound ions) estimated with MD is in excellent agreement with electrophoretic measurements. Overall, the CpHMD simulations show good agreement with the nonlinear form of the PB (NLPB) model but not with its linear form, which involves a theoretical inconsistency in the calculation of the concentration maps. In several analyses, the observed pH-dependent trends for the counterions and co-ions are those generally expected, and the ion concentration maps correctly converge to the bulk ionic strength as one moves away from the protein. Despite the overall similarity, the CpHMD and NLPB approaches show some discrepancies when analyzed in more detail, which may be related to an apparent overestimation of counterion excess and underestimation of co-ion exclusion by the NLPB model, particularly at short distances from the protein.
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3
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Khaniya U, Mao J, Wei RJ, Gunner MR. Characterizing Protein Protonation Microstates Using Monte Carlo Sampling. J Phys Chem B 2022; 126:2476-2485. [PMID: 35344367 PMCID: PMC8997239 DOI: 10.1021/acs.jpcb.2c00139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His, making up ≈25% of the residues. The protonation state of residues, cofactors, and ligands defines a "protonation microstate". In an ensemble of proteins some residues will be ionized and others neutral, leading to a mixture of protonation microstates rather than in a single one as is often assumed. The microstate distribution changes with pH. The protein environment also modifies residue proton affinity so microstate distributions change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The ΔG, ΔH, and ΔS between the four protonation states of Glu35 and Asp52 in lysozyme are shown to be calculated with reasonable precision. At pH 7 the lysozyme charge ranges from 6 to 10, with 24 accepted protonation microstates, while RCs have ≈50,000. A weighted Pearson correlation analysis shows coupling between residue protonation states in RCs and how they change when the quinone in the QB site is reduced. Protonation microstates can be used to define input MD parameters and provide insight into the motion of protons coupled to reactions.
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Affiliation(s)
- Umesh Khaniya
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - Junjun Mao
- Department of Physics, City College of New York, New York, New York 10031, United States
| | - Rongmei Judy Wei
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
| | - M R Gunner
- Department of Physics, City College of New York, New York, New York 10031, United States.,Department of Physics, The Graduate Center, City University of New York, New York, New York 10016, United States.,Department of Chemistry, The Graduate Center, City University of New York, New York, New York 10016, United States
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4
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Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.
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Affiliation(s)
- Yingying Zhang
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Kamran Haider
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Junjun Mao
- Levich Institute, School of Engineering, City College of New York, City University of New York, New York, NY 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Xuyu Zhu
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Sergei Noskov
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, AB, Canada
| | - Themis Lazaridis
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry, City College of New York, City University of New York, New York, NY 10031, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
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5
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Wang J, Perez-Cruet JM, Huang HL, Reiss K, Gisriel CJ, Banerjee G, Kaur D, Ghosh I, Dziarski A, Gunner MR, Batista VS, Brudvig GW. Identification of a Na +-Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II. Biochemistry 2020; 59:2823-2831. [PMID: 32650633 DOI: 10.1021/acs.biochem.0c00303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions and one redox-inactive Ca2+ ion, with two nearby bound Cl- ions. Sodium is a common counterion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Here, we find that the oxygen-evolution activity of spinach PSII increases with Na+ concentration, particularly at high pH. A Na+-specific binding site next to the OEC, becomes available after deprotonation of the D1-H337 amino acid residue, is suggested by the analysis of two recently published PSII cryo-electron microscopy maps in combination with quantum mechanical calculations and multiconformation continuum electrostatics simulations.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Joshua M Perez-Cruet
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Christopher J Gisriel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Divya Kaur
- Department of Physics, City College of New York (CCNY), New York, New York 10031, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alisha Dziarski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - M R Gunner
- Department of Physics, City College of New York (CCNY), New York, New York 10031, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States.,Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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6
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HAN N, ZHANG ZK, LI YH, WANG W, BIAN LJ. Spectroscopic Analysis of Chloride Ion-induced Structural Change of Bacillus Amyloliquefaciens α-Amylase. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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Kaur D, Szejgis W, Mao J, Amin M, Reiss KM, Askerka M, Cai X, Khaniya U, Zhang Y, Brudvig GW, Batista VS, Gunner MR. Relative stability of the S 2 isomers of the oxygen evolving complex of photosystem II. PHOTOSYNTHESIS RESEARCH 2019; 141:331-341. [PMID: 30941614 DOI: 10.1007/s11120-019-00637-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
The oxidation of water to O2 is catalyzed by the Oxygen Evolving Complex (OEC), a Mn4CaO5 complex in Photosystem II (PSII). The OEC is sequentially oxidized from state S0 to S4. The S2 state, (MnIII)(MnIV)3, coexists in two redox isomers: S2,g=2, where Mn4 is MnIV and S2,g=4.1, where Mn1 is MnIV. Mn4 has two terminal water ligands, whose proton affinity is affected by the Mn oxidation state. The relative energy of the two S2 redox isomers and the protonation state of the terminal water ligands are analyzed using classical multi-conformer continuum electrostatics (MCCE). The Monte Carlo simulations are done on QM/MM optimized S1 and S2 structures docked back into the complete PSII, keeping the protonation state of the protein at equilibrium with the OEC redox and protonation states. Wild-type PSII, chloride-depleted PSII, PSII in the presence of oxidized YZ/protonated D1-H190, and the PSII mutants D2-K317A, D1-D61A, and D1-S169A are studied at pH 6. The wild-type PSII at pH 8 is also described. In qualitative agreement with experiment, in wild-type PSII, the S2,g=2 redox isomer is the lower energy state; while chloride depletion or pH 8 stabilizes the S2,g=4.1 state and the mutants D2-K317A, D1-D61A, and D1-S169A favor the S2,g=2 state. The protonation states of D1-E329, D1-E65, D1-H337, D1-D61, and the terminal waters on Mn4 (W1 and W2) are affected by the OEC oxidation state. The terminal W2 on Mn4 is a mixture of water and hydroxyl in the S2,g=2 state, indicating the two water protonation states have similar energy, while it remains neutral in the S1 and S2,g=4.1 states. In wild-type PSII, advancement to S2 leads to negligible proton loss and so there is an accumulation of positive charge. In the analyzed mutations and Cl- depleted PSII, additional deprotonation is found upon formation of S2 state.
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Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Witold Szejgis
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Junjun Mao
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Muhamed Amin
- University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Krystle M Reiss
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Mikhail Askerka
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
- Department of Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
- Department of Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Yingying Zhang
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
- Department of Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - M R Gunner
- Department of Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- Department of Physics, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA.
- Department of Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
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8
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Amin M, Kaur D, Yang KR, Wang J, Mohamed Z, Brudvig GW, Gunner MR, Batista V. Thermodynamics of the S2-to-S3 state transition of the oxygen-evolving complex of photosystem II. Phys Chem Chem Phys 2019; 21:20840-20848. [DOI: 10.1039/c9cp02308a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The S2 to S3 transition in the OEC of PSII changes the structure of the Mn cluster. Monte Carlo sampling finds a Ca terminal water moves to form a bridge to Mn4 and the Mn1 ligand E189 can be replaced with a hydroxyl as a proton is lost.
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Affiliation(s)
- Muhamed Amin
- Center for Free-Electron Laser Science
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- Department of Sciences
| | - Divya Kaur
- Department of Physics
- City College of New York
- 160 Convent Avenue
- New York
- USA
| | - Ke R. Yang
- Department of Chemistry, Yale University
- New Haven
- USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry
- Yale University
- New Haven
- USA
| | - Zainab Mohamed
- Zewail City of Science and Technology
- Sheikh Zayed
- 12588 Giza
- Egypt
| | | | - M. R. Gunner
- Department of Physics
- City College of New York
- 160 Convent Avenue
- New York
- USA
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9
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Ross GA, Rustenburg AS, Grinaway PB, Fass J, Chodera JD. Biomolecular Simulations under Realistic Macroscopic Salt Conditions. J Phys Chem B 2018; 122:5466-5486. [PMID: 29649876 PMCID: PMC6078207 DOI: 10.1021/acs.jpcb.7b11734] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carlo osmostat that can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduces the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of nonequilibrium candidate Monte Carlo (NCMC) moves in which monovalent ions and water molecules are alchemically transmuted using short nonequilibrium trajectories, with a modified Metropolis-Hastings criterion ensuring correct equilibrium statistics for an ( Δμ, N, p, T) ensemble to achieve a ∼1046× boost in acceptance rates. We demonstrate how typical protein (DHFR and the tyrosine kinase Src) and nucleic acid (Drew-Dickerson B-DNA dodecamer) systems exhibit salt concentration distributions that significantly differ from fixed-salt bulk simulations and display fluctuations that are on the same order of magnitude as the average.
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Affiliation(s)
- Gregory A. Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Present address: Schrödinger, New York, NY 10036
| | - Ariën S. Rustenburg
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065
| | - Patrick B. Grinaway
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065
| | - Josh Fass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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10
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Two Cl Ions and a Glu Compete for a Helix Cage in the CLC Proton/Cl - Antiporter. Biophys J 2017; 113:1025-1036. [PMID: 28877486 DOI: 10.1016/j.bpj.2017.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 11/21/2022] Open
Abstract
The ubiquitously expressed CLC chloride transporters are involved in a great variety of physiological functions. The CLC protein fold is shared by Cl- channels and 2Cl-:1H+ antiporters. The antiporters pump three charges per cycle across the membrane with two Cl ions moving in the opposite direction of one proton. Multiconformational continuum electrostatics was used to calculate the coupled thermodynamics of the protonation of the extracellular-facing gating Glu (Ex) and Cl- binding to the external (Sx) and central (Sc) sites in CLC-ec1, the Escherichia coli exchanger. Sx, Sc, and Ex are buried within the protein where the intersection of two helix N-termini creates a region with a strong, localized positive potential for anion binding. Our chemical potential titrations describe the thermodynamic linkage for binding the Cl- to each site and protons to Ex. We find that the 2Cl-:1H+ binding stoichiometry is a result of Cl- binding to Sx requiring H+ binding to Ex, whereas Cl- binding to Sc does not lead to proton uptake. When Sx binds a Cl-, the protonated Ex moves upward, out of the positive helix cage. The increasing Ex proton affinity on binding the first Cl- reduces the cost of binding the second Cl- at either Sx or Sc. Despite the repulsion among the anions, the lowest energy states have two anions bound in the helix cage. The state with no Cl- is not favored electrostatically, but relies on Ex blocking Sx and on the central residues Y445 and S107 blocking Sc.
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11
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Mandal M, Askerka M, Banerjee G, Amin M, Brudvig GW, Batista VS, Gunner MR. Characterization of ammonia binding to the second coordination shell of the oxygen-evolving complex of photosystem II. Dalton Trans 2017; 46:16089-16095. [DOI: 10.1039/c7dt03901h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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.
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Affiliation(s)
- Manoj Mandal
- Department of Physics
- City College of New York
- C.U.N.Y. New York 10031
- USA
| | | | | | - Muhammed Amin
- Center for Free-Electron Laser Science (CFEL)
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
| | | | | | - M. R. Gunner
- Department of Physics
- City College of New York
- C.U.N.Y. New York 10031
- USA
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12
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Gunner MR, Baker NA. Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins. Methods Enzymol 2016; 578:1-20. [PMID: 27497160 DOI: 10.1016/bs.mie.2016.05.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.
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Affiliation(s)
- M R Gunner
- City College of New York in the City University of New York, New York, United States.
| | - N A Baker
- Pacific Northwest National Laboratory, Richland, DC, United States; Brown University, Providence, RI, United States
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13
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Lim SA, Ahmed MU. A label free electrochemical immunosensor for sensitive detection of porcine serum albumin as a marker for pork adulteration in raw meat. Food Chem 2016; 206:197-203. [PMID: 27041316 DOI: 10.1016/j.foodchem.2016.03.063] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 10/22/2022]
Abstract
A label free electrochemical immunosensor for sensitive detection of porcine serum albumin (PSA) is reported in this work. The immunosensor was constructed by first electrochemically reducing 4-carboxyphenyl diazonium salt, which had been electrochemically generated in situ, to a stable 4-carboxyphenyl layer on carbon nanofiber-modified screen printed electrode. Antibodies were covalently attached onto the electrode using carbodiimide chemistry between the carboxylic groups of the 4-carboxyphenyl layer and amine groups of the antibody. Using the strong affinities of serum albumins towards anions, the increase in cathodic peak current in anionic redox probe after immunocomplex formation with antibodies was used for PSA detection. The reported immunosensor demonstrated a linear range from 0.5 to 500pg/mL for the measurement of PSA with detection limit of 0.5pg/mL in buffer solution. Cross-reactivity studies have shown excellent specificity with satisfactory recovery of PSA in fresh meat samples without the need of sample dilution.
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Affiliation(s)
- Syazana Abdullah Lim
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE 1410, Brunei Darussalam; Biosensors and Biotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Daruusalam, Jalan Tungku Link, Gadong BE 1410, Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Biotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Daruusalam, Jalan Tungku Link, Gadong BE 1410, Brunei Darussalam.
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14
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Hilario E, Caulkins BG, Huang YMM, You W, Chang CEA, Mueller LJ, Dunn MF, Fan L. Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1864:268-279. [PMID: 26708480 PMCID: PMC4732270 DOI: 10.1016/j.bbapap.2015.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/20/2015] [Accepted: 12/01/2015] [Indexed: 02/02/2023]
Abstract
Four new X-ray structures of tryptophan synthase (TS) crystallized with varying numbers of the amphipathic N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) molecule are presented. These structures show one of the F6 ligands threaded into the tunnel from the β-site and reveal a distinct hydrophobic region. Over this expanse, the interactions between F6 and the tunnel are primarily nonpolar, while the F6 phosphoryl group fits into a polar pocket of the β-subunit active site. Further examination of TS structures reveals that one portion of the tunnel (T1) binds clusters of water molecules, whereas waters are not observed in the nonpolar F6 binding region of the tunnel (T2). MD simulation of another TS structure with an unobstructed tunnel also indicates the T2 region of the tunnel excludes water, consistent with a dewetted state that presents a significant barrier to the transfer of water into the closed β-site. We conclude that hydrophobic molecules can freely diffuse between the α- and β-sites via the tunnel, while water does not. We propose that exclusion of water serves to inhibit reaction of water with the α-aminoacrylate intermediate to form ammonium ion and pyruvate, a deleterious side reaction in the αβ-catalytic cycle. Finally, while most TS structures show βPhe280 partially blocking the tunnel between the α- and β-sites, new structures show an open tunnel, suggesting the flexibility of the βPhe280 side chain. Flexible docking studies and MD simulations confirm that the dynamic behavior of βPhe280 allows unhindered transfer of indole through the tunnel, therefore excluding a gating role for this residue.
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Affiliation(s)
- Eduardo Hilario
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Bethany G Caulkins
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Yu-Ming M Huang
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Wanli You
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Leonard J Mueller
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Michael F Dunn
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Li Fan
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA
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15
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Amin M, Vogt L, Szejgis W, Vassiliev S, Brudvig GW, Bruce D, Gunner MR. Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II. J Phys Chem B 2015; 119:7366-77. [PMID: 25575266 DOI: 10.1021/jp510948e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The oxygen-evolving complex (OEC) of photosystem II (PSII) is a unique Mn4O5Ca cluster that catalyzes water oxidation via four photoactivated electron transfer steps. As the protein influence on the redox and protonation chemistry of the OEC remains an open question, we present a classical valence model of the OEC that allows the redox state of each Mn and the protonation state of bridging μ-oxos and terminal waters to remain in equilibrium with the PSII protein throughout the redox cycle. We find that the last bridging oxygen loses its proton during the transition from S0 to S1. Two possible S2 states are found depending on the OEC geometry: S2 has Mn4(IV) with a proton lost from a terminal water (W1) trapped by the nearby D1-D61 if O5 is closer to Mn4, or Mn1(IV), with partial deprotonation of D1-H337 and D1-E329 if O5 is closer to Mn1. In S3, the OEC is Mn4(IV) with W2 deprotonated. The estimated OEC Em's range from +0.7 to +1.3 V, enabling oxidation by P680(+), the primary electron donor in PSII. In chloride-depleted PSII, the proton release increases during the S1 to S2 transition, leaving the OEC unable to properly advance through the water-splitting cycle.
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Affiliation(s)
- Muhamed Amin
- †Department of Physics, J-419, City College of New York, 138th Street, Convent Avenue, New York, New York 10031, United States
| | - Leslie Vogt
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Witold Szejgis
- †Department of Physics, J-419, City College of New York, 138th Street, Convent Avenue, New York, New York 10031, United States
| | - Serguei Vassiliev
- §Department of Biological Sciences, Brock University, 500 Glenridge Ave., St. Catherines, ON LS2 3A1, Canada
| | - Gary W Brudvig
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Doug Bruce
- §Department of Biological Sciences, Brock University, 500 Glenridge Ave., St. Catherines, ON LS2 3A1, Canada
| | - M R Gunner
- †Department of Physics, J-419, City College of New York, 138th Street, Convent Avenue, New York, New York 10031, United States
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16
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Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions. Proc Natl Acad Sci U S A 2014; 111:16377-82. [PMID: 25362051 DOI: 10.1073/pnas.1411119111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Key mutations differentiate the functions of homologous proteins. One example compares the inward ion pump halorhodopsin (HR) and the outward proton pump bacteriorhodopsin (BR). Of the nine essential buried ionizable residues in BR, six are conserved in HR. However, HR changes three BR acids, D85 in a central cluster of ionizable residues, D96, nearer the intracellular, and E204, nearer the extracellular side of the membrane to the small, neutral amino acids T111, V122, and T230, respectively. In BR, acidic amino acids are stationary anions whose proton affinity is modulated by conformational changes, establishing a sequence of directed binding and release of protons. Multiconformation continuum electrostatics calculations of chloride affinity and residue protonation show that, in reaction intermediates where an acid is ionized in BR, a Cl(-) is bound to HR in a position near the deleted acid. In the HR ground state, Cl(-) binds tightly to the central cluster T111 site and weakly to the extracellular T230 site, recovering the charges on ionized BR-D85 and neutral E204 in BR. Imposing key conformational changes from the BR M intermediate into the HR structure results in the loss of Cl(-) from the central T111 site and the tight binding of Cl(-) to the extracellular T230 site, mirroring the changes that protonate BR-D85 and ionize E204 in BR. The use of a mobile chloride in place of D85 and E204 makes HR more susceptible to the environmental pH and salt concentrations than BR. These studies shed light on how ion transfer mechanisms are controlled through the interplay of protein and ion electrostatics.
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17
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ProBLM web server: protein and membrane placement and orientation package. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:838259. [PMID: 25126110 PMCID: PMC4122144 DOI: 10.1155/2014/838259] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/08/2023]
Abstract
The 3D structures of membrane proteins are typically determined without the presence of a lipid bilayer. For the purpose of studying the role of membranes on the wild type characteristics of the corresponding protein, determining the position and orientation of transmembrane proteins within a membrane environment is highly desirable. Here we report a geometry-based approach to automatically insert a membrane protein with a known 3D structure into pregenerated lipid bilayer membranes with various dimensions and lipid compositions or into a pseudomembrane. The pseudomembrane is built using the Protein Nano-Object Integrator which generates a parallelepiped of user-specified dimensions made up of pseudoatoms. The pseudomembrane allows for modeling the desolvation effects while avoiding plausible errors associated with wrongly assigned protein-lipid contacts. The method is implemented into a web server, the ProBLM server, which is freely available to the biophysical community. The web server allows the user to upload a protein coordinate file and any missing residues or heavy atoms are regenerated. ProBLM then creates a combined protein-membrane complex from the given membrane protein and bilayer lipid membrane or pseudomembrane. The user is given an option to manually refine the model by manipulating the position and orientation of the protein with respect to the membrane.
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18
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Huang YMM, Chang CEA. Achieving peptide binding specificity and promiscuity by loops: case of the forkhead-associated domain. PLoS One 2014; 9:e98291. [PMID: 24870410 PMCID: PMC4037201 DOI: 10.1371/journal.pone.0098291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/30/2014] [Indexed: 11/18/2022] Open
Abstract
The regulation of a series of cellular events requires specific protein–protein interactions, which are usually mediated by modular domains to precisely select a particular sequence from diverse partners. However, most signaling domains can bind to more than one peptide sequence. How do proteins create promiscuity from precision? Moreover, these complex interactions typically occur at the interface of a well-defined secondary structure, α helix and β sheet. However, the molecular recognition primarily controlled by loop architecture is not fully understood. To gain a deep understanding of binding selectivity and promiscuity by the conformation of loops, we chose the forkhead-associated (FHA) domain as our model system. The domain can bind to diverse peptides via various loops but only interact with sequences containing phosphothreonine (pThr). We applied molecular dynamics (MD) simulations for multiple free and bound FHA domains to study the changes in conformations and dynamics. Generally, FHA domains share a similar folding structure whereby the backbone holds the overall geometry and the variety of sidechain atoms of multiple loops creates a binding surface to target a specific partner. FHA domains determine the specificity of pThr by well-organized binding loops, which are rigid to define a phospho recognition site. The broad range of peptide recognition can be attributed to different arrangements of the loop interaction network. The moderate flexibility of the loop conformation can help access or exclude binding partners. Our work provides insights into molecular recognition in terms of binding specificity and promiscuity and helpful clues for further peptide design.
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Affiliation(s)
- Yu-ming M. Huang
- Department of Chemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (YMH); (CAC)
| | - Chia-en A. Chang
- Department of Chemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (YMH); (CAC)
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19
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Fujiwara SI, Amisaki T. Fatty acid binding to serum albumin: Molecular simulation approaches. Biochim Biophys Acta Gen Subj 2013; 1830:5427-34. [DOI: 10.1016/j.bbagen.2013.03.032] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 02/02/2023]
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20
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Webb MI, Wu B, Jang T, Chard RA, Wong EWY, Wong MQ, Yapp DTT, Walsby CJ. Increasing the Bioavailability of RuIIIAnticancer Complexes through Hydrophobic Albumin Interactions. Chemistry 2013; 19:17031-42. [DOI: 10.1002/chem.201302671] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Indexed: 11/08/2022]
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21
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Bochi GV, Torbitz VD, Cargnin LP, Sangoi MB, Santos RCV, Gomes P, Moresco RN. Fructose-1,6-bisphosphate and N-acetylcysteine attenuate the formation of advanced oxidation protein products, a new class of inflammatory mediators, in vitro. Inflammation 2013; 35:1786-92. [PMID: 22777066 DOI: 10.1007/s10753-012-9498-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The accumulation of advanced oxidation protein products (AOPP) has been linked to several pathological conditions. Previous studies have identified AOPP as a novel biomarker of oxidative damage to proteins and a novel class of mediator of inflammation. The aim of this study was to determine the effects of fructose-1,6-bisphosphate (FBP) and N-acetylcysteine (NAC) as well as the synergistic effect of both treatments on the formation of AOPP in vitro. For this purpose, we incubated the human serum albumin (HSA) with various hypochlorous acid (HOCl) concentrations to produce albumin-advanced oxidation protein products (HSA-AOPP). Both FBP and NAC were capable of inhibiting the formation of HOCl-induced AOPP in a concentration-dependent manner. The synergistic effect promoted by the association of these drugs showed to be more effective than when tested alone. Thus, both FBP and NAC may be good candidates to mitigate and neutralize pro-inflammatory and pro-oxidant effects of AOPP in several diseases.
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Affiliation(s)
- Guilherme Vargas Bochi
- Laboratório de Bioquímica Clínica, Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal de Santa Maria, Avenida Roraima 1000, Prédio 26, Sala 1401, Camobi, 97105-900 Santa Maria, Rio Grande do Sul, Brazil
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22
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Amin M, Vogt L, Vassiliev S, Rivalta I, Sultan MM, Bruce D, Brudvig GW, Batista VS, Gunner MR. Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II. J Phys Chem B 2013; 117:6217-26. [PMID: 23570540 DOI: 10.1021/jp403321b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The influence of electrostatic interactions on the free energy of proton coupled electron transfer in biomimetic oxomanganese complexes inspired by the oxygen-evolving complex (OEC) of photosystem II (PSII) are investigated. The reported study introduces an enhanced multiconformer continuum electrostatics (MCCE) model, parametrized at the density functional theory (DFT) level with a classical valence model for the oxomanganese core. The calculated pKa's and oxidation midpoint potentials (E(m)'s) match experimental values for eight complexes, indicating that purely electrostatic contributions account for most of the observed couplings between deprotonation and oxidation state transitions. We focus on pKa's of terminal water ligands in [Mn(II/III)(H2O)6](2+/3+) (1), [Mn(III)(P)(H2O)2](3-) (2, P = 5,10,15,20-tetrakis(2,6-dichloro-3-sulfonatophenyl)porphyrinato), [Mn2(IV,IV)(μ-O)2(terpy)2(H2O)2](4+) (3, terpy = 2,2':6',2″-terpyridine), and [Mn3(IV,IV,IV)(μ-O)4(phen)4(H2O)2](4+) (4, phen = 1,10-phenanthroline) and the pKa's of μ-oxo bridges and Mn E(m)'s in [Mn2(μ-O)2(bpy)4] (5, bpy = 2,2'-bipyridyl), [Mn2(μ-O)2(salpn)2] (6, salpn = N,N'-bis(salicylidene)-1,3-propanediamine), [Mn2(μ-O)2(3,5-di(Cl)-salpn)2] (7), and [Mn2(μ-O)2(3,5-di(NO2)-salpn)2] (8). The analysis of complexes 6-8 highlights the strong coupling between electron and proton transfers, with any Mn oxidation lowering the pKa of an oxo bridge by 10.5 ± 0.9 pH units. The model also accounts for changes in the E(m)'s by ligand substituents, such as found in complexes 6-8, due to the electron withdrawing Cl (7) and NO2 (8). The reported study provides the foundation for analysis of electrostatic effects in other oxomanganese complexes and metalloenzymes, where proton coupled electron transfer plays a fundamental role in redox-leveling mechanisms.
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Affiliation(s)
- Muhamed Amin
- Department of Physics, City College of New York, New York, New York 10031, United States
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23
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Harris JR, Soliakov A, Lewis RJ. In vitro fibrillogenesis of collagen type I in varying ionic and pH conditions. Micron 2013; 49:60-8. [PMID: 23582981 DOI: 10.1016/j.micron.2013.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/20/2013] [Accepted: 03/17/2013] [Indexed: 11/24/2022]
Abstract
Collagen is the most abundant protein in the human body, and has primary roles in the formation of tendons, cartilage and bone, it provides mechanical strength to skin and indeed almost every organ and muscle is associated with a layer of collagen. It is thus a key component of the extracellular matrix. Here we have studied the in vitro fibrillogenesis of acetic acid-soluble collagen type I under physiological and varying non-physiological conditions by TEM from negatively stained specimens. At pH 2.5 the collagen heterotrimer remains soluble at increasing buffer concentrations and in the presence of increasing NaCl concentrations. At pH 4.5 molecular aggregates form at low NaCl concentrations, but at higher NaCl concentrations fibrils with a diffuse ~11 nm banding are formed. At pH 7.0, initial molecular aggregates form at low NaCl concentrations that progressively form characteristic ~67 nm D-banded collagen fibrils at intermediate NaCl concentrations that cluster to form thicker multi-fibril D-banded fibres in higher NaCl concentrations. By contrast, increasing concentrations of sodium phosphate at pH 7.0 leads to the formation of flexuous, unbanded fibrils at higher concentrations from the initial, loosely aggregated form of collagen. At higher pHs, the formation of D-banded fibrils is less efficient, particularly at pH 9.0. Thus at neutral pH, the presence of chloride anions, rather than sodium cations, is required for the production of D-banded collagen fibrils; higher than normal physiological chloride concentrations in the form of NaCl or Tris·HCl at neutral pH, but not phosphate buffer, can also lead to the efficient in vitro formation of D-banded collagen fibrils.
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Affiliation(s)
- J Robin Harris
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne NE2 4HH, UK.
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24
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Huang YMM, Kang M, Chang CEA. Mechanistic insights into phosphopeptide--BRCT domain association: preorganization, flexibility, and phosphate recognition. J Phys Chem B 2012; 116:10247-58. [PMID: 22857521 DOI: 10.1021/jp305028d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Promiscuous proteins are commonly observed in biological systems, for example, in modular domains that recognize phosphopeptides during signal transduction. This promiscuous recognition is of fundamental interest in chemistry and biology but is challenging when designing phosphopeptides in silico for cell biology studies. To investigate promiscuous recognition and binding processes of phosphopeptides and the modular domain, we selected a domain essential in breast cancer-the breast-cancer-associated protein 1 (BRCA1) C-terminal (BRCT) repeats as our model system. We performed molecular dynamics simulations and detailed analyses of the dihedral space to study protein fluctuation and conformational changes with phosphopeptide binding. We also studied the association processes of phosphorylated and unphosphorylated peptides using Brownian dynamics with a coarse-grained model. We found that the BRCT domain is preorganized for phosphopeptide binding but has a moderate arrangement of side chains to form complexes with various types of phosphopeptides. Phosphopeptide binding restricts the system motion in general, while the nonpolar phosphopeptide becomes more flexible in the bound state. Our analysis found that the BRCT domain utilizes different mechanisms, usually termed lock and key, induced-fit, and population-shift/conformational-selection models, to recognize peptides with different features. Brownian dynamics simulations revealed that the charged phosphate group may not always accelerate peptide association processes, but it helps the phosphopeptide orient into binding pockets accurately and stabilizes the complex. This work provides insights into molecular recognition in the promiscuous protein system.
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Affiliation(s)
- Yu-ming M Huang
- Department of Chemistry, University of California , Riverside, California 92521, United States
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25
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Bell SG, Yang W, Tan ABH, Zhou R, Johnson EOD, Zhang A, Zhou W, Rao Z, Wong LL. The crystal structures of 4-methoxybenzoate bound CYP199A2 and CYP199A4: structural changes on substrate binding and the identification of an anion binding site. Dalton Trans 2012; 41:8703-14. [PMID: 22695988 DOI: 10.1039/c2dt30783a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of the 4-methoxybenzoate bound forms of cytochrome P450 enzymes CYP199A2 and CYP199A4 from the Rhodopseudomonas palustris strains CGA009 and HaA2 have been solved. The structures of these two enzymes, which share 86% sequence identity, are very similar though some differences are found on the proximal surface. In these structures the enzymes have a closed conformation, in contrast to the substrate-free form of CYP199A2 where an obvious substrate access channel is observed. The switch from an open to a closed conformation arises from pronounced residue side-chain movements and alterations of ion pair and hydrogen bonding interactions at the entrance of the access channel. A chloride ion bound just inside the protein surface caps the entrance to the active site and protects the substrate and the heme from the external solvent. In both structures the substrate is held in place via hydrophobic and hydrogen bond interactions. The methoxy group is located over the heme iron, accounting for the high activity and selectivity of these enzymes for oxidative demethylation of the substrate. Mutagenesis studies on CYP199A4 highlight the involvement of hydrophobic (Phe185) and hydrophilic (Arg92, Ser95 and Arg243) amino acid residues in the binding of para-substituted benzoates by these enzymes.
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Affiliation(s)
- Stephen G Bell
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
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26
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Feliks M, Ullmann GM. Glycerol Dehydratation by the B12-Independent Enzyme May Not Involve the Migration of a Hydroxyl Group: A Computational Study. J Phys Chem B 2012; 116:7076-87. [DOI: 10.1021/jp301165b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikolaj Feliks
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
| | - G. Matthias Ullmann
- Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447
Bayreuth, Germany
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27
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Madeo J, Mihajlovic M, Lazaridis T, Gunner MR. Slow dissociation of a charged ligand: analysis of the primary quinone Q(A) site of photosynthetic bacterial reaction centers. J Am Chem Soc 2011; 133:17375-85. [PMID: 21863833 PMCID: PMC3202297 DOI: 10.1021/ja205811f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Indexed: 12/14/2022]
Abstract
Reaction centers (RCs) are integral membrane proteins that undergo a series of electron transfer reactions during the process of photosynthesis. In the Q(A) site of RCs from Rhodobacter sphaeroides, ubiquinone-10 is reduced, by a single electron transfer, to its semiquinone. The neutral quinone and anionic semiquinone have similar affinities, which is required for correct in situ reaction thermodynamics. A previous study showed that despite similar affinities, anionic quinones associate and dissociate from the Q(A) site at rates ≈10(4) times slower than neutral quinones indicating that anionic quinones encounter larger binding barriers (Madeo, J.; Gunner, M. R. Modeling binding kinetics at the Q(A) site in bacterial reaction centers. Biochemistry 2005, 44, 10994-11004). The present study investigates these barriers computationally, using steered molecular dynamics (SMD) to model the unbinding of neutral ground state ubiquinone (UQ) and its reduced anionic semiquinone (SQ(-)) from the Q(A) site. In agreement with experiment, the SMD unbinding barrier for SQ(-) is larger than for UQ. Multi Conformational Continuum Electrostatics (MCCE), used here to calculate the binding energy, shows that SQ(-) and UQ have comparable affinities. In the Q(A) site, there are stronger binding interactions for SQ(-) compared to UQ, especially electrostatic attraction to a bound non-heme Fe(2+). These interactions compensate for the higher SQ(-) desolvation penalty, allowing both redox states to have similar affinities. These additional interactions also increase the dissociation barrier for SQ(-) relative to UQ. Thus, the slower SQ(-) dissociation rate is a direct physical consequence of the additional binding interactions required to achieve a Q(A) site affinity similar to that of UQ. By a similar mechanism, the slower association rate is caused by stronger interactions between SQ(-) and the polar solvent. Thus, stronger interactions for both the unbound and bound states of charged and highly polar ligands can slow their binding kinetics without a conformational gate. Implications of this for other systems are discussed.
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Affiliation(s)
- Jennifer Madeo
- Departments of Physics and Chemistry, City College of New York, New York, New York 10031, United States
| | - Maja Mihajlovic
- Departments of Physics and Chemistry, City College of New York, New York, New York 10031, United States
| | - Themis Lazaridis
- Departments of Physics and Chemistry, City College of New York, New York, New York 10031, United States
| | - M. R. Gunner
- Departments of Physics and Chemistry, City College of New York, New York, New York 10031, United States
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Rivalta I, Amin M, Luber S, Vassiliev S, Pokhrel R, Umena Y, Kawakami K, Shen JR, Kamiya N, Bruce D, Brudvig GW, Gunner MR, Batista VS. Structural-functional role of chloride in photosystem II. Biochemistry 2011; 50:6312-5. [PMID: 21678923 DOI: 10.1021/bi200685w] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.
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Affiliation(s)
- Ivan Rivalta
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.
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29
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Huang YMM, Chang CEA. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics. BMC BIOPHYSICS 2011; 4:12. [PMID: 21612598 PMCID: PMC3146460 DOI: 10.1186/2046-1682-4-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 05/25/2011] [Indexed: 11/25/2022]
Abstract
Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions. Results Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA) or in combination with α-helix (BRCT repeats) or β-sheet (WW domain) fail to differentiate pThr/pSer. Conclusions Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside, CA92521, USA.
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Dumit VI, Cortez N, Matthias Ullmann G. Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid. Proteins 2011; 79:2076-85. [PMID: 21538544 DOI: 10.1002/prot.23027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 02/08/2011] [Accepted: 02/25/2011] [Indexed: 11/12/2022]
Abstract
Flavin-containing reductases are involved in a wide variety of physiological reactions such as photosynthesis, nitric oxide synthesis, and detoxification of foreign compounds, including therapeutic drugs. Ferredoxin-NADP(H)-reductase (FNR) is the prototypical enzyme of this family. The fold of this protein is highly conserved and occurs as one domain of several multidomain enzymes such as the members of the diflavin reductase family. The enzymes of this family have emerged as fusion of a FNR and a flavodoxin. Although the active sites of these enzymes are very similar, different enzymes function in opposite directions, that is, some reduce oxidized nicotinamide adenine dinucleotide phosphate (NADP(+)) and some oxidize reduced nicotinamide adenine dinucleotide phosphate (NADPH). In this work, we analyze the protonation behavior of titratable residues of these enzymes through electrostatic calculations. We find that a highly conserved carboxylic acid in the active site shows a different titration behavior in different flavin reductases. This residue is deprotonated in flavin reductases present in plastids, but protonated in bacterial counterparts and in diflavin reductases. The protonation state of the carboxylic acid may also influence substrate binding. The physiological substrate for plastidic enzymes is NADP(+), but it is NADPH for the other mentioned reductases. In this article, we discuss the relevance of the environment of this residue for its protonation and its importance in catalysis. Our results allow to reinterpret and explain experimental data.
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Affiliation(s)
- Verónica I Dumit
- Structural Biology/Bioinformatics, University of Bayreuth, 95447 Bayreuth, Germany
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31
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Stranzl GR, Santelli E, Bankston LA, La Clair C, Bobkov A, Schwarzenbacher R, Godzik A, Perego M, Grynberg M, Liddington RC. Structural insights into inhibition of Bacillus anthracis sporulation by a novel class of non-heme globin sensor domains. J Biol Chem 2011; 286:8448-8458. [PMID: 21216948 DOI: 10.1074/jbc.m110.207126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pathogenesis by Bacillus anthracis requires coordination between two distinct activities: plasmid-encoded virulence factor expression (which protects vegetative cells from immune surveillance during outgrowth and replication) and chromosomally encoded sporulation (required only during the final stages of infection). Sporulation is regulated by at least five sensor histidine kinases that are activated in response to various environmental cues. One of these kinases, BA2291, harbors a sensor domain that has ∼35% sequence identity with two plasmid proteins, pXO1-118 and pXO2-61. Because overexpression of pXO2-61 (or pXO1-118) inhibits sporulation of B. anthracis in a BA2291-dependent manner, and pXO2-61 expression is strongly up-regulated by the major virulence gene regulator, AtxA, it was suggested that their function is to titrate out an environmental signal that would otherwise promote untimely sporulation. To explore this hypothesis, we determined crystal structures of both plasmid-encoded proteins. We found that they adopt a dimeric globin fold but, most unusually, do not bind heme. Instead, they house a hydrophobic tunnel and hydrophilic chamber that are occupied by fatty acid, which engages a conserved arginine and chloride ion via its carboxyl head group. In vivo, these domains may therefore recognize changes in fatty acid synthesis, chloride ion concentration, and/or pH. Structure-based comparisons with BA2291 suggest that it binds ligand and dimerizes in an analogous fashion, consistent with the titration hypothesis. Analysis of newly sequenced bacterial genomes points to the existence of a much broader family of non-heme, globin-based sensor domains, with related but distinct functionalities, that may have evolved from an ancestral heme-linked globin.
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Affiliation(s)
- Gudrun R Stranzl
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Eugenio Santelli
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Laurie A Bankston
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Chandra La Clair
- the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, and
| | - Andrey Bobkov
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Robert Schwarzenbacher
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Adam Godzik
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037
| | - Marta Perego
- the Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, and
| | - Marcin Grynberg
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037,; the Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Robert C Liddington
- From the Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037,.
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32
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Zheng Z, Dutton PL, Gunner MR. The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers. Proteins 2010; 78:2638-54. [PMID: 20607696 DOI: 10.1002/prot.22779] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quinones play important roles in mitochondrial and photosynthetic energy conversion acting as intramembrane, mobile electron, and proton carriers between catalytic sites in various electron transfer proteins. They display different affinity, selectivity, functionality, and exchange dynamics in different binding sites. The computational analysis of quinone binding sheds light on the requirements for quinone affinity and specificity. The affinities of 10 oxidized, neutral benzoquinones were measured for the high affinity Q(A) site in the detergent-solubilized Rhodobacter sphaeroides bacterial photosynthetic reaction center. Multiconformation Continuum Electrostatics was then used to calculate their relative binding free energies by grand canonical Monte Carlo sampling with a rigid protein backbone, flexible ligand, and side chain positions and protonation states. Van der Waals and torsion energies, Poisson-Boltzmann continuum electrostatics, and accessible surface area-dependent ligand-solvent interactions are considered. An initial, single cycle of GROMACS backbone optimization improves the match with experiment as do coupled-ligand and side-chain motions. The calculations match experiment with an root mean square deviation (RMSD) of 2.29 and a slope of 1.28. The affinities are dominated by favorable protein-ligand van der Waals rather than electrostatic interactions. Each quinone appears in a closely clustered set of positions. Methyl and methoxy groups move into the same positions as found for the native quinone. Difficulties putting methyls into methoxy sites are observed. Calculations using a solvent-accessible surface area-dependent implicit van der Waals interaction smoothed out small clashes, providing a better match to experiment with a RMSD of 0.77 and a slope of 0.97.
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Affiliation(s)
- Zhong Zheng
- Department of Physics, City College of New York, New York, New York 10031, USA
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33
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Fatmi MQ, Chang CEA. The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase. PLoS Comput Biol 2010; 6:e1000994. [PMID: 21085641 PMCID: PMC2978696 DOI: 10.1371/journal.pcbi.1000994] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 10/08/2010] [Indexed: 11/25/2022] Open
Abstract
The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS). TRPS uses a set of α/β–dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand–bound conformations. Our simulations also revealed that the α/β–dimeric unit stabilizes the substrate–protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function. Conformational changes of enzymes are often related to regulating and creating an optimal environment for efficient chemistry. An increasing number of evidences also indicate that oligomerization/co-localization of proteins contributes to the efficiency of metabolic pathways. Although static structures have been available for many multi-enzyme complexes, their efficiency is also governed by the synergistic regulation between the multi-units. Our study applies molecular dynamics and Brownian dynamics simulations to the model system, the tryptophan synthase complex. The multi-enzyme complex is a bienzyme nanomachine and its catalytic activity is intimately related to the allosteric signaling and the metabolite transfer between its α– and β–subunits connected by a 25-Å long channel. Our studies suggest that the binding partner is crucial for the ligand binding processes. Although the isolated monomers are stable in the ligand–free state and can form stable interaction if the substrate is in the final bound conformation, it has higher energy barrier when ligand binds to the active site. We also show that the channel does not always exist, but it may be blocked before the enzyme reaches its final bound conformation. The results highlight the importance of forming protein complexes and the cooperative changes during different states.
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Affiliation(s)
- M. Qaiser Fatmi
- Department of Chemistry, University of California, Riverside, Riverside, California, United States of America
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, California, United States of America
- * E-mail:
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34
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Duran C, Thompson CH, Xiao Q, Hartzell HC. Chloride channels: often enigmatic, rarely predictable. Annu Rev Physiol 2010; 72:95-121. [PMID: 19827947 DOI: 10.1146/annurev-physiol-021909-135811] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Until recently, anion (Cl(-)) channels have received considerably less attention than cation channels. One reason for this may be that many Cl(-) channels perform functions that might be considered cell-biological, like fluid secretion and cell volume regulation, whereas cation channels have historically been associated with cellular excitability, which typically happens more rapidly. In this review, we discuss the recent explosion of interest in Cl(-) channels, with special emphasis on new and often surprising developments over the past five years. This is exemplified by the findings that more than half of the ClC family members are antiporters, and not channels, as was previously thought, and that bestrophins, previously prime candidates for Ca(2+)-activated Cl(-) channels, have been supplanted by the newly discovered anoctamins and now hold a tenuous position in the Cl(-) channel world.
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Affiliation(s)
- Charity Duran
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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35
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Fatmi MQ, Ai R, Chang CEA. Synergistic Regulation and Ligand-Induced Conformational Changes of Tryptophan Synthase. Biochemistry 2009; 48:9921-31. [DOI: 10.1021/bi901358j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Qaiser Fatmi
- Department of Chemistry, University of California, Riverside, California 92521
| | - Rizi Ai
- Department of Chemistry, University of California, Riverside, California 92521
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, California 92521
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