1
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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2
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Lawson KE, Dekle JK, Adamczyk AJ. Towards pharmaceutical protein stabilization: DFT and statistical learning studies on non-enzymatic peptide hydrolysis degradation mechanisms. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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3
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Kubo S, Takada S. Rotational Mechanism of F O Motor in the F-Type ATP Synthase Driven by the Proton Motive Force. Front Microbiol 2022; 13:872565. [PMID: 35783438 PMCID: PMC9243769 DOI: 10.3389/fmicb.2022.872565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
In FOF1 ATP synthase, driven by the proton motive force across the membrane, the FO motor rotates the central rotor and induces conformational changes in the F1 motor, resulting in ATP synthesis. Recently, many near-atomic resolution structural models have been obtained using cryo-electron microscopy. Despite high resolution, however, static information alone cannot elucidate how and where the protons pass through the FO and how proton passage is coupled to FO rotation. Here, we review theoretical and computational studies based on FO structure models. All-atom molecular dynamics (MD) simulations elucidated changes in the protonation/deprotonation of glutamate-the protein-carrier residue-during rotation and revealed the protonation states that form the "water wire" required for long-range proton hopping. Coarse-grained MD simulations unveiled a free energy surface based on the protonation state and rotational angle of the rotor. Hybrid Monte Carlo and MD simulations showed how proton transfer is coupled to rotation.
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Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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4
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Gagkayeva ZV, Gorshunov BP, Kachesov AY, Motovilov KA. Infrared fingerprints of water collective dynamics indicate proton transport in biological systems. Phys Rev E 2022; 105:044409. [PMID: 35590571 DOI: 10.1103/physreve.105.044409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
Recent publications on spectroscopy of water layers in water bridge structures revealed a significant enhancement of the proton mobility and the dielectric contribution of translational vibrations of water molecules in the interfacial layers compared to bulk water. Herewith, the results of long-term studies of proton dynamics in solid-state acids have shown that proton mobility increases significantly with the predominance of hydronium, but not Zundel, cations in the aqueous phase. In the present work, in the light of these data, we reanalyzed our previously published results on broadband dielectric spectroscopy of bovine heart cytochrome c, bovine serum albumin, and the extracellular matrix and filaments of Shewanella oneidensis MR-1. We revealed that, just as in water bridges, an increase in electrical conductivity in these systems correlates with an increase in the dielectric contribution of water molecular translational vibrations. In addition, the appearance of spectral signatures of the hydronium cations was observed only in those cases when the system revealed noticeable electrical conductivity due to delocalized charge carriers.
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Affiliation(s)
- Z V Gagkayeva
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - B P Gorshunov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - A Ye Kachesov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - K A Motovilov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
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5
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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6
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Sakashita N, Ishikita H, Saito K. Rigidly hydrogen-bonded water molecules facilitate proton transfer in photosystem II. Phys Chem Chem Phys 2020; 22:15831-15841. [PMID: 32613215 DOI: 10.1039/d0cp00295j] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the water-splitting enzyme photosystem II (PSII), the proton is released from the catalytic site and transferred to the protein bulk surface via the proton-relay mechanism. Proton transfer occurs in a proton-conducting channel consisting of a series of water molecules connected by hydrogen-bonded (H-bonded) chains. The water-transport protein aquaporin (AQP) also contains a water chain with structure similar to that of the PSII proton channel, although the water chain does not transport protons. We compared the PSII proton channel with the AQP water channel from the following standpoints: (1) the energetics of proton transfer based on crystal structures obtained from quantum mechanical/molecular mechanical calculations, and (2) fluctuations in water molecules obtained from molecular dynamics simulations. The results showed that residues facing the channel and acting as H-bonded partners of water molecules predominantly determined the proton-transfer ability. In PSII, the water chain is surrounded by H-bond acceptors (e.g., carbonyl groups), and the water chain transports protons where the water molecules are rigidly fixed. In AQP, the water chain is surrounded by hydrophobic sidechains or H-bond donors (e.g., NH2 groups), and it does not transport protons where the water molecules are flexible and fluctuating.
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Affiliation(s)
- Naoki Sakashita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan and Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan and Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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7
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Misztal T, Golaszewska A, Branska-Januszewska J, Marcinczyk N, Chabielska E, Tomasiak M, Rusak T. HAuCl 4, Putative General Aquaporins Blocker, Reduces Platelet Spreading, Filopodia Formation, Procoagulant Response, and Thrombus Formation Under Flow. Front Physiol 2020; 11:1025. [PMID: 32973556 PMCID: PMC7472438 DOI: 10.3389/fphys.2020.01025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/27/2020] [Indexed: 02/04/2023] Open
Abstract
Background: Recent studies indicate that aquaporin (AQP) water channels have a regulatory function in human platelet secretion and in procoagulant response of murine platelets. However, the engagement of AQPs in morphological changes, procoagulant response, and thrombus formation in human blood has never been investigated. Methods: Confocal microscopy was used to study platelet spreading, filopodia formation, ballooning, and thrombus formation under flow. Flow cytometry was utilized to assess platelet phosphatidylserine (PS) exposure and microparticles shedding. Kinetics of clot formation in vitro was evaluated by thromboelastometry. Mouse model of ferric chloride (III) (FeCl3)-induced thrombosis was used to investigate thrombus formation in vivo. Results: We found that chloroauric(III) acid (HAuCl4), a classical AQP inhibitor (10–100 μM), reduced spreading of human platelets on collagen-coated surfaces and inhibited filopodia formation in a fluid phase. Under flow conditions, HAuCl4 (100 μM) attenuated thrombi growth on collagen, platelet secretion, and PS exposure. Thrombus formation was restored by the addition of exogenous adenosine diphosphate (ADP). Collagen-evoked platelet procoagulant response (evaluated as PS exposure, shedding of microparticles, platelet-dependent thrombin generation, and membrane ballooning) was distinctly reduced by HAuCl4 (25–200 μM), as well as the dynamics of clot formation. In mouse model of thrombosis, reduction of surface of PS-positive cells within thrombus was observed in the presence of HAuCl4 (1–10 mg/kg). Conclusion: These results suggest that in human platelets AQPs are crucial for agonist-evoked morphological changes, thrombus formation under flow, and in development of procoagulant response. Antithrombotic effect in vivo suggests that nontoxic inhibitors of AQPs may be considered as potential candidates for a novel class of antiplatelet drugs.
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Affiliation(s)
- Tomasz Misztal
- Department of Physical Chemistry, Medical University of Bialystok, Bialystok, Poland
| | - Agata Golaszewska
- Department of Physical Chemistry, Medical University of Bialystok, Bialystok, Poland
| | | | - Natalia Marcinczyk
- Department of Biopharmacy, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Chabielska
- Department of Biopharmacy, Medical University of Bialystok, Bialystok, Poland
| | - Marian Tomasiak
- Department of Physical Chemistry, Medical University of Bialystok, Bialystok, Poland
| | - Tomasz Rusak
- Department of Physical Chemistry, Medical University of Bialystok, Bialystok, Poland
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8
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Williamson G, Tamburrino G, Bizior A, Boeckstaens M, Dias Mirandela G, Bage MG, Pisliakov A, Ives CM, Terras E, Hoskisson PA, Marini AM, Zachariae U, Javelle A. A two-lane mechanism for selective biological ammonium transport. eLife 2020; 9:57183. [PMID: 32662768 PMCID: PMC7447429 DOI: 10.7554/elife.57183] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
The transport of charged molecules across biological membranes faces the dual problem of accommodating charges in a highly hydrophobic environment while maintaining selective substrate translocation. This has been the subject of a particular controversy for the exchange of ammonium across cellular membranes, an essential process in all domains of life. Ammonium transport is mediated by the ubiquitous Amt/Mep/Rh transporters that includes the human Rhesus factors. Here, using a combination of electrophysiology, yeast functional complementation and extended molecular dynamics simulations, we reveal a unique two-lane pathway for electrogenic NH4+ transport in two archetypal members of the family, the transporters AmtB from Escherichia coli and Rh50 from Nitrosomonas europaea. The pathway underpins a mechanism by which charged H+ and neutral NH3 are carried separately across the membrane after NH4+ deprotonation. This mechanism defines a new principle of achieving transport selectivity against competing ions in a biological transport process.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Mélanie Boeckstaens
- Biology of Membrane Transport Laboratory, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Gaëtan Dias Mirandela
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Marcus G Bage
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Andrei Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Eilidh Terras
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Anna Maria Marini
- Biology of Membrane Transport Laboratory, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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9
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Wragg D, de Almeida A, Casini A, Leoni S. Unveiling the Mechanisms of Aquaglyceroporin‐3 Water and Glycerol Permeation by Metadynamics. Chemistry 2019; 25:8713-8718. [DOI: 10.1002/chem.201902121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Darren Wragg
- School of ChemistryCardiff University Park Place CF10 3AT Cardiff UK
| | - Andreia de Almeida
- Tumour Micro Environment Group, Division of Cancer and GeneticsSchool of MedicineCardiff University Tenovus Building Cardiff CF14 4XN UK
| | - Angela Casini
- School of ChemistryCardiff University Park Place CF10 3AT Cardiff UK
| | - Stefano Leoni
- School of ChemistryCardiff University Park Place CF10 3AT Cardiff UK
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10
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On the control of the proton current in the voltage-gated proton channel Hv1. Proc Natl Acad Sci U S A 2018; 115:10321-10326. [PMID: 30254162 DOI: 10.1073/pnas.1809766115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The nature of the action of voltage-activated proton transport proteins is a conundrum of great current interest. Here we approach this issue by exploring the action of Hv1, a voltage-gated proton channel found in different cells in humans and other organisms. Our study focuses on evaluating the free energy of transporting a proton through the channel, as well as the effect of the proton transfer through D112, in both the closed and open channel conformations. It is found that D112 allows a transported proton to bypass the electrostatic barrier of the open channel, while not being able to help in passing the barrier in the closed form. This reflects the change in position of the gating arginine residues relative to D112, upon voltage activation. Significantly, the effect of D112 accounts for the observed trend in selectivity by overcoming the electrostatic barrier at its highest point. Thus, the calculations provide a structure/function correlation for the Hv1 system. The present work also clarifies that the action of Hv1 is not controlled by a Grotthuss mechanism but, as is always the case, by the protein electrostatic potential at the rate-limiting barriers.
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11
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Liu Z, Stecher T, Oberhofer H, Reuter K, Scheurer C. Response properties at the dynamic water/dichloroethane liquid–liquid interface. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1504132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Zhu Liu
- Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
| | - Thomas Stecher
- Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
| | - Harald Oberhofer
- Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
| | - Karsten Reuter
- Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
| | - Christoph Scheurer
- Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
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12
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Basu S. CP dock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics. J Mol Model 2017; 24:8. [PMID: 29218430 DOI: 10.1007/s00894-017-3546-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 11/24/2017] [Indexed: 01/18/2023]
Abstract
The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6.2 or higher) in the computation of electrostatic complementarity to make the validation tool physico-chemically more realistic. The two methods (single- and multi-dielectric) agree decently in their resultant Em values, and hence, provisions for both methods have been kept in the software suite. So to speak, the global electrostatic balance within a well-folded protein and/or a well-packed interface seems only marginally perturbed by the choice of different internal dielectric values. However, both from theoretical as well as practical grounds, the more advanced multi-dielectric version of the plot is certainly recommended for potentially producing more reliable results. The report also presents a new methodology and a variant plot, namely CPdock, based on the same principles of complementarity specifically designed to be used in the docking of proteins. The efficacy of the method to discriminate between good and bad docked protein complexes has been tested on a recent state-of-the-art docking benchmark. The results unambiguously indicate that CPdock can indeed be effective in the initial screening phase of a docking scoring pipeline before going into more sophisticated and computationally expensive scoring functions. CPdock has been made available at https://github.com/nemo8130/CPdock . Graphical Abstract An example showing the efficacy of CPdock to be used in the initial screening phase of a protein-protein docking scoring pipeline.
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Affiliation(s)
- Sankar Basu
- Department of Chemistry, University of Delhi, New Delhi, India.
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13
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Yoon H, Kolev V, Warshel A. Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. J Phys Chem B 2017; 121:9358-9365. [PMID: 28911225 PMCID: PMC5954165 DOI: 10.1021/acs.jpcb.7b07726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The study of the function of proteins on a quantitative level requires consideration of the water molecules in and around the protein. This requirement presents a major computational challenge due to the fact that the insertion of water molecules can have a very high activation barrier and would require a long simulation time. Recently, we developed a water flooding (WF) approach which is based on a postprocessing Monte Carlo ranking of possible water configurations. This approach appears to provide a very effective way for assessing the insertion free energies and determining the most likely configurations of the internal water molecules. Although the WF approach was used effectively in modeling challenging systems that have not been addressed reliably by other microscopic approaches, it was not validated by a comparison to the more rigorous grand canonical Monte Carlo (GCMC) method. Here we validate the WF approach by comparing its performance to that of the GCMC method. It is found that the WF approach reproduces the GCMC results in well-defined test cases but does so much faster. This established the WF approach as a useful strategy for finding correct water configurations in proteins and thus to provide a powerful way for studies of the functions of proteins.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California , 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089-1062, United States
| | - Vesselin Kolev
- Department of Chemistry, University of Southern California , 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California , 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089-1062, United States
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14
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Du J, Wang X, Nie Q, Yang J, Yao X. Computational study of the binding mechanism of medium chain acyl-CoA synthetase with substrate in Methanosarcina acetivorans. J Biotechnol 2017; 259:160-167. [PMID: 28751277 DOI: 10.1016/j.jbiotec.2017.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/19/2017] [Accepted: 07/22/2017] [Indexed: 02/03/2023]
Abstract
The acyl-AMP forming family of adenylating enzymes catalyzes the formation of acyl-CoA from an acyl substrate, ATP, and CoA, which is a metabolite of many catabolic and anabolic processes. The medium-chain acyl-CoA synthetase from Methanosarcina acetivorans, designated MacsMa, uses 2-methylbutyrate as its preferred substrate. It is reported that the interaction between the sidechain of Cys298 and Lys256 of this enzyme is important for the catalytic activity. The mutation of these residues resulted in the changes of the structure stability and the reduced or absence catalytic activity. In the present study, the binding mechanism between the substrate 2-methylbutyrate- AMP (2MeBA) and MacsMa were explored by integrating multiple computational methods including molecular docking, molecular dynamics simulations, binding free energy calculation, active site access channel analysis and principal component analysis. The binding free energy between WT, mutated Macs and substrate was calculated by MM-GBSA method, which indicated that the binding affinity between this enzyme and substrate was stronger in the WT than that in the mutated forms (K256L, K256T and C298Y). Per-residue binding free energy decomposition identified some residues, such as Gly327, Phe350, Gly351, Gln352 and Lys461, which are important for the enzyme and substrate binding affinity. The access channels of the mutant system (MacsK256L, MacsK256T and MacsC298Y) were found to be different from those in the wild-type systems. It suggested that K256L and C298Y induced larger flexibility to the overall protein compared with the WT, whereas K256T induced larger flexibility to the partial protein compared with the WT by PCA vector porcupines. This study provides novel insight to understand the substrate binding mechanism of Macs and useful information for the rational enzyme design.
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Affiliation(s)
- Juan Du
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiaolu Wang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Qingjuan Nie
- Foreign Languages School, Qingdao Agricultural University, Qingdao, China
| | - Jianming Yang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, China.
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
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15
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Du J, Wang X, Dong CH, Yang JM, Yao XJ. Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana. PLoS One 2016; 11:e0159053. [PMID: 27414648 PMCID: PMC4944973 DOI: 10.1371/journal.pone.0159053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/27/2016] [Indexed: 12/15/2022] Open
Abstract
Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1–actin complex, we constructed a homology model of the AtADF1–actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson–Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin.
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Affiliation(s)
- Juan Du
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
- * E-mail:
| | - Xue Wang
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Chun-Hai Dong
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Jian Ming Yang
- Key Laboratory of Plant Biotechnology of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiao Jun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
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16
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Lu X, Fang D, Ito S, Okamoto Y, Ovchinnikov V, Cui Q. QM/MM free energy simulations: recent progress and challenges. MOLECULAR SIMULATION 2016; 42:1056-1078. [PMID: 27563170 DOI: 10.1080/08927022.2015.1132317] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Shingo Ito
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Boston, MA 02138
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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17
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Esteva-Font C, Jin BJ, Lee S, Phuan PW, Anderson MO, Verkman AS. Experimental Evaluation of Proposed Small-Molecule Inhibitors of Water Channel Aquaporin-1. Mol Pharmacol 2016; 89:686-93. [PMID: 26993802 DOI: 10.1124/mol.116.103929] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/17/2016] [Indexed: 12/20/2022] Open
Abstract
The aquaporin-1 (AQP1) water channel is a potentially important drug target, as AQP1 inhibition is predicted to have therapeutic action in edema, tumor growth, glaucoma, and other conditions. Here, we measured the AQP1 inhibition efficacy of 12 putative small-molecule AQP1 inhibitors reported in six recent studies, and one AQP1 activator. Osmotic water permeability was measured by stopped-flow light scattering in human and rat erythrocytes that natively express AQP1, in hemoglobin-free membrane vesicles from rat and human erythrocytes, and in plasma membrane vesicles isolated from AQP1-transfected Chinese hamster ovary cell cultures. As a positive control, 0.3 mM HgCl2 inhibited AQP1 water permeability by >95%. We found that none of the tested compounds at 50 µM significantly inhibited or increased AQP1 water permeability in these assays. Identification of AQP1 inhibitors remains an important priority.
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Affiliation(s)
- Cristina Esteva-Font
- Departments of Medicine and Physiology, University of California, San Francisco, California (C.E.-F., B.-J.J., S.L., P.-W.P., A.S.V.); Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California (M.O.A.)
| | - Byung-Ju Jin
- Departments of Medicine and Physiology, University of California, San Francisco, California (C.E.-F., B.-J.J., S.L., P.-W.P., A.S.V.); Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California (M.O.A.)
| | - Sujin Lee
- Departments of Medicine and Physiology, University of California, San Francisco, California (C.E.-F., B.-J.J., S.L., P.-W.P., A.S.V.); Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California (M.O.A.)
| | - Puay-Wah Phuan
- Departments of Medicine and Physiology, University of California, San Francisco, California (C.E.-F., B.-J.J., S.L., P.-W.P., A.S.V.); Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California (M.O.A.)
| | - Marc O Anderson
- Departments of Medicine and Physiology, University of California, San Francisco, California (C.E.-F., B.-J.J., S.L., P.-W.P., A.S.V.); Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California (M.O.A.)
| | - A S Verkman
- Departments of Medicine and Physiology, University of California, San Francisco, California (C.E.-F., B.-J.J., S.L., P.-W.P., A.S.V.); Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California (M.O.A.)
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18
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Ashwinder K, Kho MT, Chee PM, Lim WZ, Yap IKS, Choi SB, Yam WK. Targeting Heat Shock Proteins 60 and 70 of Toxoplasma gondii as a Potential Drug Target: In Silico Approach. Interdiscip Sci 2015; 8:374-387. [PMID: 26297309 DOI: 10.1007/s12539-015-0107-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/27/2015] [Accepted: 06/04/2015] [Indexed: 11/26/2022]
Abstract
Heat shock proteins (Hsps) 60 and 70 are postulated as a potential drug target for toxoplasmosis due to its importance in the developmental and survival of Toxoplasma gondii (T. gondii). As of today, there have been no reports on three-dimensional (3D) structure of Hsp60 and Hsp70 deposited in the Brookhaven Protein Data Bank. Hence, this study was conducted to predict 3D structures for Hsp60 and Hsp70 in T. gondii by homology modeling. Selection of the best predicted model was done based on multiple scoring functions. In addition, virtual screening was performed to short-list chemical compounds from the National Cancer Institute (NCI) Diversity Set III in search of potential inhibitor against Hsp60 and Hsp70 in T. gondii. Prior to virtual screening, binding sites of Hsp60 and Hsp70 were predicted using various servers and were used as the center in docking studies. The Hsps were docked against known natural ligands to validate the method used in estimating free energy of binding (FEB) and possible interactions between ligand and protein. Virtual screening was performed with a total of 1560 compounds from the NCI Diversity Set III. The compounds were ranked subsequently according to their FEB. Molecular basis of interactions of the top five ranked compounds was investigated using Ligplot+. The major interactions exhibited were hydrogen bonding and hydrophobic interactions in binding to Hsp60 and Hsp70. The results obtained provided information and guidelines for the development of inhibitors for Hsp60 and Hsp70 in T. gondii.
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Affiliation(s)
- Kaur Ashwinder
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Mee Teck Kho
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Phui Mun Chee
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Wui Zhuan Lim
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Ivan K S Yap
- Life Sciences Department, School of Pharmacy, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Sy Bing Choi
- Natural Product and Drug Discovery Centre, Malaysian Institutes of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Penang, Malaysia
| | - Wai Keat Yam
- Life Sciences Department, School of Pharmacy, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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19
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Espinoza-Fonseca LM, Ramírez-Salinas GL. Microsecond Molecular Simulations Reveal a Transient Proton Pathway in the Calcium Pump. J Am Chem Soc 2015; 137:7055-8. [PMID: 26028459 DOI: 10.1021/jacs.5b03814] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The calcium pump sarcoplasmic reticulum Ca(2+)-ATPase (SERCA) counter-transports Ca(2+) and H(+) at the expense of ATP hydrolysis. SERCA uses separate proton and metal ion pathways during active transport to neutralize the highly charged transport site, thus preserving SERCA's structural stability during active Ca(2+) transport. Although separate metal ion and proton pathways have been identified during slow (millisecond) structural transitions of SERCA, the existence of simultaneous metal and proton pathways during fast (microsecond) structural transitions remains unknown. We have analyzed microsecond-long trajectories of E1·H(+)771, a protonated intermediate of the pump populated during SERCA regulation. We found a transiently established hydrophobic pore in the luminal side of the transmembrane helices 6, 8, and 9. This narrow (0.5-0.6 nm) pore connects the transport sites to the sarcoplasmic reticulum lumen through a chain of water molecules. Protein pKa calculations of the transport site residues and structural analysis of the water molecules showed that this pore is suitable for proton transport. This transient proton pathway ensures neutralization of the transport sites during the rapid structural transitions associated with regulation of the pump. We conclude that this transient proton pathway plays a central role in optimizing active Ca(2+) transport by SERCA. Our discovery provides insight into ion-exchange mechanisms through transient hydrophobic pores in P-type ATPases.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- †Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - G Lizbeth Ramírez-Salinas
- ‡Laboratorio de Modelado Molecular y Bioinformática, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
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20
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Wallerstein J, Weininger U, Khan MAI, Linse S, Akke M. Site-specific protonation kinetics of acidic side chains in proteins determined by pH-dependent carboxyl (13)C NMR relaxation. J Am Chem Soc 2015; 137:3093-101. [PMID: 25665463 DOI: 10.1021/ja513205s] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-transfer dynamics plays a critical role in many biochemical processes, such as proton pumping across membranes and enzyme catalysis. The large majority of enzymes utilize acid-base catalysis and proton-transfer mechanisms, where the rates of proton transfer can be rate limiting for the overall reaction. However, measurement of proton-exchange kinetics for individual side-chain carboxyl groups in proteins has been achieved in only a handful of cases, which typically have involved comparative analysis of mutant proteins in the context of reaction network modeling. Here we describe an approach to determine site-specific protonation and deprotonation rate constants (kon and koff, respectively) of carboxyl side chains, based on (13)C NMR relaxation measurements as a function of pH. We validated the method using an extensively studied model system, the B1 domain of protein G, for which we measured rate constants koff in the range (0.1-3) × 10(6) s(-1) and kon in the range (0.6-300) × 10(9) M(-1) s(-1), which correspond to acid-base equilibrium dissociation constants (Ka) in excellent agreement with previous results determined by chemical shift titrations. Our results further reveal a linear free-energy relationship between log kon and pKa, which provides information on the free-energy landscape of the protonation reaction, showing that the variability among residues in these parameters arises primarily from the extent of charge stabilization of the deprotonated state by the protein environment. We find that side-chain carboxyls with extreme values of koff or kon are involved in hydrogen bonding, thus providing a mechanistic explanation for the observed stabilization of the protonated or deprotonated state.
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Affiliation(s)
- Johan Wallerstein
- Department of Biophysical Chemistry and ‡Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University , P.O. Box 124, SE-221 00 Lund, Sweden
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21
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Goyal P, Yang S, Cui Q. Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci 2015; 6:826-841. [PMID: 25678950 PMCID: PMC4321873 DOI: 10.1039/c4sc01674b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps.
Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps. For the proton pump cytochrome c oxidase, while the regulation of thermodynamic driving force for key proton transfers has been discussed in great detail, the microscopic basis for the control of proton transfer kinetics has been poorly understood. Here we carry out extensive QM/MM free energy simulations to probe the kinetics of relevant proton transfer steps and analyze the effects of local structure and hydration level. We show that protonation of the proton loading site (PLS, taken to be a propionate of heme a3) requires a concerted process in which a key glutamic acid (Glu286H) delivers the proton to the PLS while being reprotonated by an excess proton coming from the D-channel. The concerted nature of the mechanism is a crucial feature that enables the loading of the PLS before the cavity containing Glu286 is better hydrated to lower its pKa to experimentally measured range; the charged rather than dipolar nature of the process also ensures a tight coupling with heme a reduction, as emphasized by Siegbahn and Blomberg. In addition, we find that rotational flexibility of the PLS allows its protonation before that of the binuclear center (the site where oxygen gets reduced to water). Together with our recent study (P. Goyal, et al., Proc. Natl. Acad. Sci. U. S. A., 2013, 110, 18886–18891) that focused on the modulation of Glu286 pKa, the current work suggests a mechanism that builds in a natural sequence for the protonation of the PLS prior to that of the binuclear center. This provides microscopic support to the kinetic constraints revealed by kinetic network analysis as essential elements that ensure an efficient vectorial proton transport in cytochrome c oxidase.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Shuo Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
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22
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Klein N, Neumann J, O'Neil JD, Schneider D. Folding and stability of the aquaglyceroporin GlpF: Implications for human aqua(glycero)porin diseases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:622-33. [PMID: 25462169 DOI: 10.1016/j.bbamem.2014.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 01/22/2023]
Abstract
Aquaporins are highly selective polytopic transmembrane channel proteins that facilitate the permeation of water across cellular membranes in a large diversity of organisms. Defects in aquaporin function are associated with common diseases, such as nephrogenic diabetes insipidus, congenital cataract and certain types of cancer. In general, aquaporins have a highly conserved structure; from prokaryotes to humans. The conserved structure, together with structural dynamics and the structural framework for substrate selectivity is discussed. The folding pathway of aquaporins has been a topic of several studies in recent years. These studies revealed that a conserved protein structure can be reached by following different folding pathways. Based on the available data, we suggest a complex folding pathway for aquaporins, starting from the insertion of individual helices up to the formation of the tetrameric aquaporin structure. The consequences of some known mutations in human aquaporin-encoding genes, which most likely affect the folding and stability of human aquaporins, are discussed.
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Affiliation(s)
- Noreen Klein
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Jennifer Neumann
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Joe D O'Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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23
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Bartosik A, Wiśniewska M, Makowski M. Potentials of mean force for hydrophobic interactions between hydrocarbons in water solution: dependence on temperature, solute shape, and solute size. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Angelika Bartosik
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Marta Wiśniewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry; University of Gdańsk; Wita Stwosza 63 80-308 Gdańsk Poland
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24
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Goyal P, Qian HJ, Irle S, Lu X, Roston D, Mori T, Elstner M, Cui Q. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B 2014; 118:11007-27. [PMID: 25166899 PMCID: PMC4174991 DOI: 10.1021/jp503372v] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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25
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Mechanisms of molecular transport through the urea channel of Helicobacter pylori. Nat Commun 2014; 4:2900. [PMID: 24305683 PMCID: PMC3863980 DOI: 10.1038/ncomms3900] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/08/2013] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori survival in acidic environments relies on cytoplasmic hydrolysis of gastric urea into ammonia and carbon dioxide, which buffer the pathogen’s periplasm. Urea uptake is greatly enhanced and regulated by HpUreI, a proton-gated inner membrane channel protein essential for gastric survival of H. pylori. The crystal structure of HpUreI describes a static snapshot of the channel with two constriction sites near the center of the bilayer that are too narrow to allow passage of urea or even water. Here we describe the urea transport mechanism at atomic resolution, revealed by unrestrained microsecond equilibrium molecular dynamics simulations of the hexameric channel assembly. Two consecutive constrictions open to allow conduction of urea, which is guided through the channel by interplay between conserved residues that determine proton rejection and solute selectivity. Remarkably, HpUreI conducts water at rates equivalent to aquaporins, which might be essential for efficient transport of urea at small concentration gradients. Helicobacter pylori survives in the acidic environment of the stomach by taking up urea and converting it to ammonia and carbon dioxide, which buffer the bacterial periplasm. Using molecular dynamics simulations, McNulty et al. provide insight into the mechanism of urea uptake through the H. pylori urea transporter.
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26
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Repič M, Purg M, Vianello R, Mavri J. Examining Electrostatic Preorganization in Monoamine Oxidases A and B by Structural Comparison and pKa Calculations. J Phys Chem B 2014; 118:4326-32. [DOI: 10.1021/jp500795p] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Matej Repič
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
| | - Miha Purg
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
| | - Robert Vianello
- Quantum
Organic Chemistry Group, Ruđer Bošković Institute, Bijenička
cesta 54, HR−10000 Zagreb, Croatia
| | - Janez Mavri
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
- EN−FIST Centre of Excellence, Dunajska 156, SI−1000 Ljubljana, Slovenia
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27
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Abstract
The aquaporins (AQPs) are a family of small, integral membrane proteins that facilitate water transport across the plasma membranes of cells in response to osmotic gradients. Data from knockout mice support the involvement of AQPs in epithelial fluid secretion, cell migration, brain oedema and adipocyte metabolism, which suggests that modulation of AQP function or expression could have therapeutic potential in oedema, cancer, obesity, brain injury, glaucoma and several other conditions. Moreover, loss-of-function mutations in human AQPs cause congenital cataracts (AQP0) and nephrogenic diabetes insipidus (AQP2), and autoantibodies against AQP4 cause the autoimmune demyelinating disease neuromyelitis optica. Although some potential AQP modulators have been identified, challenges associated with the development of better modulators include the druggability of the target and the suitability of the assay methods used to identify modulators.
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28
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Zhang Z, Wu T, Wang Q, Pan H, Tang R. Impact of interfacial high-density water layer on accurate estimation of adsorption free energy by Jarzynski's equality. J Chem Phys 2014; 140:034706. [DOI: 10.1063/1.4858428] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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29
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Ishikita H, Saito K. Proton transfer reactions and hydrogen-bond networks in protein environments. J R Soc Interface 2013; 11:20130518. [PMID: 24284891 DOI: 10.1098/rsif.2013.0518] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKa values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pKa matching condition and allow for proton transfer reactions, proteins often adjust the pKa via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.
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Affiliation(s)
- Hiroshi Ishikita
- Department of Biological Sciences, Graduate School of Science, Osaka University, , Machikaneyama-cho 1-1, Toyonaka 560-0043, Japan
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30
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Gosink LJ, Hogan EA, Pulsipher TC, Baker NA. Bayesian model aggregation for ensemble-based estimates of protein pKa values. Proteins 2013; 82:354-63. [PMID: 23946048 DOI: 10.1002/prot.24390] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/26/2013] [Indexed: 12/14/2022]
Abstract
This article investigates an ensemble-based technique called Bayesian Model Averaging (BMA) to improve the performance of protein amino acid pKa predictions. Structure-based pKa calculations play an important role in the mechanistic interpretation of protein structure and are also used to determine a wide range of protein properties. A diverse set of methods currently exist for pKa prediction, ranging from empirical statistical models to ab initio quantum mechanical approaches. However, each of these methods are based on a set of conceptual assumptions that can effect a model's accuracy and generalizability for pKa prediction in complicated biomolecular systems. We use BMA to combine eleven diverse prediction methods that each estimate pKa values of amino acids in staphylococcal nuclease. These methods are based on work conducted for the pKa Cooperative and the pKa measurements are based on experimental work conducted by the García-Moreno lab. Our cross-validation study demonstrates that the aggregated estimate obtained from BMA outperforms all individual prediction methods with improvements ranging from 45 to 73% over other method classes. This study also compares BMA's predictive performance to other ensemble-based techniques and demonstrates that BMA can outperform these approaches with improvements ranging from 27 to 60%. This work illustrates a new possible mechanism for improving the accuracy of pKa prediction and lays the foundation for future work on aggregate models that balance computational cost with prediction accuracy.
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Affiliation(s)
- Luke J Gosink
- Pacific Northwest National Laboratory, Computational and Statistical Analytics Division, MSID K7-2, Richland, Washington, 99352
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31
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Pore waters regulate ion permeation in a calcium release-activated calcium channel. Proc Natl Acad Sci U S A 2013; 110:17332-7. [PMID: 24101457 DOI: 10.1073/pnas.1316969110] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The recent crystal structure of Orai, the pore unit of a calcium release-activated calcium (CRAC) channel, is used as the starting point for molecular dynamics and free-energy calculations designed to probe this channel's conduction properties. In free molecular dynamics simulations, cations localize preferentially at the extracellular channel entrance near the ring of Glu residues identified in the crystal structure, whereas anions localize in the basic intracellular half of the pore. To begin to understand ion permeation, the potential of mean force (PMF) was calculated for displacing a single Na(+) ion along the pore of the CRAC channel. The computed PMF indicates that the central hydrophobic region provides the major hindrance for ion diffusion along the permeation pathway, thereby illustrating the nonconducting nature of the crystal structure conformation. Strikingly, further PMF calculations demonstrate that the mutation V174A decreases the free energy barrier for conduction, rendering the channel effectively open. This seemingly dramatic effect of mutating a nonpolar residue for a smaller nonpolar residue in the pore hydrophobic region suggests an important role for the latter in conduction. Indeed, our computations show that even without significant channel-gating motions, a subtle change in the number of pore waters is sufficient to reshape the local electrostatic field and modulate the energetics of conduction, a result that rationalizes recent experimental findings. The present work suggests the activation mechanism for the wild-type CRAC channel is likely regulated by the number of pore waters and hence pore hydration governs the conductance.
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Kepp KP. O2Binding to Heme is Strongly Facilitated by Near-Degeneracy of Electronic States. Chemphyschem 2013; 14:3551-8. [DOI: 10.1002/cphc.201300658] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Indexed: 11/06/2022]
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Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, Facciotti MT. Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway. Structure 2013; 21:290-7. [PMID: 23394942 DOI: 10.1016/j.str.2012.12.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 12/08/2012] [Accepted: 12/12/2012] [Indexed: 11/18/2022]
Abstract
Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained a mystery. From an analysis of the X-ray structure of the D96G/F171C/F219L triple mutant of bR and 60 independent molecular dynamics simulations of bR photointermediates, we report that the deprotonation of D96, a key residue in proton transfer reactions, serves two roles that occur sequentially. First, D96 donates a proton to the Schiff base. Subsequently, the deprotonation of D96 serves to "unlatch" the cytoplasmic side. The latching function of D96 appears to be remarkably robust, functioning to open hydration channels in all photointermediate structures. These results suggest that the protonation state of D96 may be the critical biophysical cue controlling the opening and closing of the cytoplasmic half-channel in bR. We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality.
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Affiliation(s)
- Ting Wang
- Genome Center and Department of Biomedical Engineering, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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McGrath MJ, Kuo IFW, Hayashi S, Takada S. Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations. J Am Chem Soc 2013; 135:8908-19. [PMID: 23751065 DOI: 10.1021/ja401540g] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ~0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the Pγ-Oβ dissociation concerted with approach of the lytic water to PγO3-. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO(4)2- via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism.
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Affiliation(s)
- Matthew J McGrath
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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35
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Balme S, Picaud F, Kraszewski S, Déjardin P, Janot JM, Lepoitevin M, Capomanes J, Ramseyer C, Henn F. Controlling potassium selectivity and proton blocking in a hybrid biological/solid-state polymer nanoporous membrane. NANOSCALE 2013; 5:3961-3968. [PMID: 23535870 DOI: 10.1039/c3nr00564j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Specific separations of protons and cations are usually performed by electromembrane processes, which require external electric energy. An easier process would be using a membrane able to separate both entities by passive diffusion. Presently, such synthetic nanoporous membranes do not exist. Here, we report the production of a robust hybrid biological/artificial solid-state membrane, which allows selective permeation of alkali metal cations without competing or concurrent permeation of protons. This membrane is simple to prepare and is based on the hydrophobic nature of the polymeric pore walls, and the confined gramicidin A molecules within. This work opens a new route for separation in the domain of nanobiofiltration, especially for tunable nanodevices based on differential ion conduction, with a fundamental understanding of the confinement mechanism.
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Affiliation(s)
- Sébastien Balme
- Institut Européen des Membranes, UMR5635 CNRS-UM2-ENSCM, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
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36
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Li L, Li C, Zhang Z, Alexov E. On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi. J Chem Theory Comput 2013; 9:2126-2136. [PMID: 23585741 PMCID: PMC3622359 DOI: 10.1021/ct400065j] [Citation(s) in RCA: 362] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Indexed: 01/26/2023]
Abstract
![]()
Implicit methods for modeling protein
electrostatics require dielectric
properties of the system to be known, in particular, the value of
the dielectric constant of protein. While numerous values of the internal
protein dielectric constant were reported in the literature, still
there is no consensus of what the optimal value is. Perhaps this is
due to the fact that the protein dielectric constant is not a “constant”
but is a complex function reflecting the properties of the protein’s
structure and sequence. Here, we report an implementation of a Gaussian-based
approach to deliver the dielectric constant distribution throughout
the protein and surrounding water phase by utilizing the 3D structure
of the corresponding macromolecule. In contrast to previous reports,
we construct a smooth dielectric function throughout the space of
the system to be modeled rather than just constructing a “Gaussian
surface” or smoothing molecule–water boundary. Analysis
on a large set of proteins shows that (a) the average dielectric constant
inside the protein is relatively low, about 6–7, and reaches
a value of about 20–30 at the protein’s surface, and
(b) high average local dielectric constant values are associated with
charged residues while low dielectric constant values are automatically
assigned to the regions occupied by hydrophobic residues. In terms
of energetics, a benchmarking test was carried out against the experimental
pKa’s of 89 residues in staphylococcal
nuclease (SNase) and showed that it results in a much better RMSD
(= 1.77 pK) than the corresponding calculations done
with a homogeneous high dielectric constant with an optimal value
of 10 (RMSD = 2.43 pK).
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Affiliation(s)
- Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina 29634, United States
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Prasad BR, Plotnikov NV, Warshel A. Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping. J Phys Chem B 2012. [PMID: 23198768 DOI: 10.1021/jp309778n] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nature and mechanism of phosphate hydrolysis reactions are of great interest in view of the crucial role of these reactions in key biological processes. Although it is becoming clearer that the ultimate way of resolving mechanistic controversies must involve reliable theoretical studies, it is not widely realized that such studies cannot be performed at present by using most existing automated ways and that only careful systematic studies can lead to meaningful conclusions. The present work clarifies the above point by considering the hydrolysis of phosphate monoesters. The clarification starts by defining the actual issues that should be addressed in careful studies and by highlighting the problems with studies that ignore the need for unique mechanistic definitions (e.g., works that confuse associative and dissociative pathways). We then focus on the analysis of the proton transfer (PT) pathways in phosphate hydrolysis and on recent suggestions that PT involves more than one water molecule. Here we point out that most of the studies that found a proton transfer through several water molecules have not involved a sufficient systematic search of the relevant reaction coordinates. This includes both energy minimization approaches as well as a recent metadynamics (MTD) simulation study. To illustrate the crucial need of exploring the potential surfaces reliably, rather than relying on automated approaches, we present here a very careful study of the free energy landscape along a 3D reaction coordinate (RC) exploring both the standard 2D RC, comprised of the attacking and leaving group reaction coordinates, as well as of the proton transfer (PT) coordinate. Our study points out that QM/MM minimization or MTD studies that concluded that the hydrolysis of phosphate monoesters involves a PT through several water molecules, have not explored carefully the single water (1W) path (that involves a direct PT form the attacking water molecule to the phosphate oxygen). Furthermore, we identified the most likely reason for the difficulty in finding the 1W path by QM/MM minimization methods, as well as by the current MTD simulations. We also discuss the problems with current studies that challenge the phosphate as a base mechanism and emphasize that all recent studies found associative/concerted paths (although many have not realized the meaning of their results). Finally, although we clearly do not have the last word about the 1W versus 2W paths we believe that we illustrated that the crucial mechanistic problems with alternative pathways should not be resolved by just running black box search approaches.
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Affiliation(s)
- B Ram Prasad
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
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38
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Semimicroscopic investigation of active site pK a values in peptidylarginine deiminase 4. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1293-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Frushicheva MP, Mukherjee S, Warshel A. Electrostatic origin of the catalytic effect of a supramolecular host catalyst. J Phys Chem B 2012; 116:13353-60. [PMID: 23088306 DOI: 10.1021/jp3084327] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of enzyme mimetic catalysts as well as the analysis of the catalytic effects of such catalysts has been a major challenge for synthetic chemists. One of the impressive examples of artificial catalysts has been the development of a highly charged host compound that provides a significant acceleration to the hydrolysis of orthoformates and other systems. However, the origin of the catalytic effect has not been quantified, and its origin remains somewhat unclear. The understanding of the corresponding supramolecular catalysis has thus become a major challenge, both in terms of computational modeling and in terms of the analysis of the corresponding acid-catalyzed reaction. Here we present a computer simulation study and kinetic analyses that reproduce the experimentally observed catalytic effect, establishing that this effect is due to electrostatic stabilization of the positively charged transition state (relative to the uncharged bound complex). Our study illustrates the crucial need for careful analysis of the complex kinetics of the catalytic effect and the host system, as well as the need for computational modeling in analyzing the catalytic effect and in the potential design of better catalysts. Finally, our finding of the large stabilization of the bound H(3)O(+) points out the very low "local pH" inside the host system even when the solvent is kept at a high pH.
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Affiliation(s)
- Maria P Frushicheva
- Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
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40
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Zienau J, Cui Q. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems. J Phys Chem B 2012; 116:12522-34. [DOI: 10.1021/jp308218m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jan Zienau
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue,
Madison, Wisconsin 53706, United States
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41
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Chakrabarty S, Warshel A. Capturing the energetics of water insertion in biological systems: the water flooding approach. Proteins 2012; 81:93-106. [PMID: 22911614 DOI: 10.1002/prot.24165] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/07/2012] [Accepted: 08/15/2012] [Indexed: 02/02/2023]
Abstract
Consistent description of the effect of internal water in proteins has been a major challenge for both simulation and experimental studies. Describing this effect has been particularly important and elusive in cases of charges in protein interiors. Here, we present a new microscopic method that provides an efficient way for simulating the energetics of water insertion. Instead of performing explicit Monte Carlo (MC) moves on the insertion process, which generally involves an enormous number of rejected attempts, our method is based on generating trial configurations with excess amount of internal water, estimating the relevant free energy by the linear response approximation, and then using a postprocessing MC treatment to filter out a limited number of configurations from a large possible set. Our approach is validated on particularly challenging test cases including the pK(a) of the V66D mutation in Staphylococcal nuclease, Glu286 in cytochrome c oxidase (CcO) and the energetics of a protonated water molecule in the D channel of CcO. The new postprocessing method allows us to reproduce the relevant energetics of highly unstable charges in protein interiors using fully microscopic calculations and provides a substantial improvement over regular microscopic free energy estimates. This advance established the effectiveness of our water insertion strategy in challenging cases that have not been addressed successfully by other microscopic methods. Furthermore, our study provides a new exciting view on the crucial effect of water penetration in key biological systems as well as a new view on the nature of the dielectric in protein interiors.
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Affiliation(s)
- Suman Chakrabarty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
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42
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Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase. PLoS Comput Biol 2012; 8:e1002674. [PMID: 22956904 PMCID: PMC3431322 DOI: 10.1371/journal.pcbi.1002674] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/22/2012] [Indexed: 01/25/2023] Open
Abstract
Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N2O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb3 oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed. Denitrification is an anaerobic process performed by several bacteria as an alternative to aerobic respiration. A key intermediate step is catalyzed by the nitric oxide reductase (NOR) enzyme, which is situated in the cytoplasmic membrane. Proton delivery to the catalytic site inside NOR is an important part of its functioning. In this work we use molecular dynamics simulations to describe water distribution and to identify proton transfer pathways in cNOR. Our results reveal two channels from the periplasmic side of the membrane and none from the cytoplasmic side, indicating that cNOR is not a proton pump. It is our hope that these results will provide a basis for further experimental and computational studies aimed to understand details of the NOR mechanism. Furthermore, this work sheds light on the molecular evolution of respiratory enzymes.
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43
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Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. Proc Natl Acad Sci U S A 2012; 109:14876-81. [PMID: 22927379 DOI: 10.1073/pnas.1212841109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular origin of the action of the F(0) proton gradient-driven rotor presents a major puzzle despite significant structural advances. Although important conceptual models have provided guidelines of how such systems should work, it has been challenging to generate a structure-based molecular model using physical principles that will consistently lead to the unidirectional proton-driven rotational motion during ATP synthesis. This work uses a coarse-grained (CG) model to simulate the energetics of the F(0)-ATPase system in the combined space defined by the rotational coordinate and the proton transport (PTR) from the periplasmic side (P) to the cytoplasmic side (N). The model establishes the molecular origin of the rotation, showing that this effect is due to asymmetry in the energetics of the proton path rather than only the asymmetry of the interaction of the Asp on the c-ring helices and Arg on the subunit-a. The simulation provides a clear conceptual background for further exploration of the electrostatic basis of proton-driven mechanochemical systems.
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44
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Benga G. The first discovered water channel protein, later called aquaporin 1: molecular characteristics, functions and medical implications. Mol Aspects Med 2012; 33:518-34. [PMID: 22705445 DOI: 10.1016/j.mam.2012.06.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 06/07/2012] [Indexed: 02/08/2023]
Abstract
After a decade of work on the water permeability of red blood cells (RBC) Benga group in Cluj-Napoca, Romania, discovered in 1985 the first water channel protein in the RBC membrane. The discovery was reported in publications in 1986 and reviewed in subsequent years. The same protein was purified by chance by Agre group in Baltimore, USA, in 1988, who called in 1991 the protein CHIP28 (CHannel forming Integral membrane Protein of 28 kDa), suggesting that it may play a role in linkage of the membrane skeleton to the lipid bilayer. In 1992 the Agre group identified CHIP28's water transport property. One year later CHIP28 was named aquaporin 1, abbreviated as AQP1. In this review the molecular structure-function relationships of AQP1 are presented. In the natural or model membranes AQP1 is in the form of a homotetramer, however, each monomer has an independent water channel (pore). The three-dimensional structure of AQP1 is described, with a detailed description of the channel (pore), the molecular mechanisms of permeation through the channel of water molecules and exclusion of protons. The permeability of the pore to gases (CO(2), NH(3), NO, O(2)) and ions is also mentioned. I have also reviewed the functional roles and medical implications of AQP1 expressed in various organs and cells (microvascular endothelial cells, kidney, central nervous system, eye, lacrimal and salivary glands, respiratory apparatus, gastrointestinal tract, hepatobiliary compartments, female and male reproductive system, inner ear, skin). The role of AQP1 in cell migration and angiogenesis in relation with cancer, the genetics of AQP1 and mutations in human subjects are also mentioned. The role of AQP1 in red blood cells is discussed based on our comparative studies of water permeability in over 30 species.
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Affiliation(s)
- Gheorghe Benga
- First Laboratory of Genetic Explorations, Cluj County Clinical Emergency Hospital, Cluj-Napoca, Romania.
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45
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Borštnar R, Repič M, Kamerlin SCL, Vianello R, Mavri J. Computational Study of the pKa Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B. J Chem Theory Comput 2012; 8:3864-70. [PMID: 26593027 DOI: 10.1021/ct300119u] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Monoamine oxidase (MAO), which exists in two isozymic forms, MAO A and MAO B, is an important flavoenzyme responsible for the metabolism of amine neurotransmitters such as dopamine, serotonin, and norepinephrine. Despite extensive research effort, neither the catalytic nor the inhibition mechanisms of MAO have been completely understood. There has also been dispute with regard to the protonation state of the substrate upon entering the active site, as well as the identity of residues that are important for the initial deprotonation of irreversible acetylenic inhibitors, in accordance with the recently proposed mechanism. Therefore, in order to investigate features essential for the modes of action of MAO, we have calculated pKa values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the substrate (as well as the pKa of the dopamine itself in the active site). The calculated pKa values for Tyr188, Tyr398, and Tyr435 in the complex are found to be shifted upward to 13.0, 13.7, and 14.7, respectively, relative to 10.1 in aqueous solution, ruling out the likelihood that they are viable proton acceptors. The altered tyrosine pKa values could be rationalized as an interplay of two opposing effects: insertion of positively charged bulky dopamine that lowers tyrosine pKa values, and subsequent removal of water molecules from the active site that elevates tyrosine pKa values, in which the latter prevails. Additionally, the pKa value of the bound dopamine (8.8) is practically unchanged compared to the corresponding value in aqueous solution (8.9), as would be expected from a charged amine placed in a hydrophobic active site consisting of aromatic moieties. We also observed potentially favorable cation-π interactions between the -NH3(+) group on dopamine and aromatic moieties, which provide a stabilizing effect to the charged fragment. Thus, we offer here theoretical evidence that the amine is most likely to be present in the active site in its protonated form, which is similar to the conclusion from experimental studies of MAO A (Jones et al. J. Neural Trans.2007, 114, 707-712). However, the free energy cost of transferring the proton from the substrate to the bulk solvent is only 1.9 kcal mol(-1), leaving open the possibility that the amine enters the chemical step in its neutral form. In conjunction with additional experimental and computational work, the data presented here should lead toward a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.
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Affiliation(s)
- Rok Borštnar
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Matej Repič
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Shina Caroline Lynn Kamerlin
- Department of Cell and Molecular Biology, Uppsala University , Uppsala Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Robert Vianello
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Quantum Organic Chemistry Group, Ruđer Bošković Institute , Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Janez Mavri
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence , Dunajska 156, SI-1000 Ljubljana, Slovenia
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Hu G, Chen LY, Wang J. Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z. J Mol Model 2012; 18:3731-41. [PMID: 22392432 DOI: 10.1007/s00894-012-1379-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 02/10/2012] [Indexed: 10/28/2022]
Abstract
Aquaporin Z (AQPZ) is a tetrameric protein that forms water channels in the cell membrane of Escherichia coli. The histidine residue (residue 174) in the selectivity filter (SF) region plays an important role in the transport of water across the membrane. In this work, we perform equilibrium molecular dynamics (MD) simulations to illustrate the gating mechanism of the SF and the influences of residue 174 in two different protonation states: Hsd174 with the proton at Nδ, and Hse174 with the proton at Nε. We calculate the pore radii in the SF region versus the simulation time. We perform steered MD to compute the free-energy profile, i.e., the potential of mean force (PMF) of a water molecule through the SF region. We conduct a quantum mechanics calculation of the binding energy of one water molecule with the residues in the SF region. The hydrogen bonds formed between the side chain of Hsd174 and the side chain of residue 189 (Arg189) play important roles in the selectivity mechanism of AQPZ. The radii of the pores, the hydrogen-bond analysis, and the free energies show that it is easier for water molecules to permeate through the SF region of AQPZ with residue 174 in the Hse state than in the Hsd state.
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Affiliation(s)
- Guodong Hu
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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47
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Ishikita H, Eger BT, Okamoto K, Nishino T, Pai EF. Protein conformational gating of enzymatic activity in xanthine oxidoreductase. J Am Chem Soc 2012; 134:999-1009. [PMID: 22145797 PMCID: PMC3264664 DOI: 10.1021/ja207173p] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 Å resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.
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Affiliation(s)
- Hiroshi Ishikita
- Career-Path Promotion Unit for Young Life Scientists, Kyoto University, 202 Building E, Graduate School of Medicine, Kyoto 606-8501, Japan.
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Abstract
Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK(a) calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 Å) and Glu46-pCA (2.57 Å). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms. (ii) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (iii) The calculated pK(a) values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK(a) difference was unlikely to satisfy the prerequisite for LBHB. (iv) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK(a) of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.
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Riccardi D, Zhu X, Goyal P, Yang S, Hou G, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4458-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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50
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Yang S, Cui Q. Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase. Biophys J 2011; 101:61-9. [PMID: 21723815 DOI: 10.1016/j.bpj.2011.05.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 01/08/2023] Open
Abstract
One of the key unresolved issues regarding proton pumping in cytochrome c oxidase (CcO) is the identity of the gating element that prevents the backflow of protons. In this study, we analyze two popular proposals for this element: isomerization of the key branching residue (Glu-286) and (re)orientation of water molecules in the hydrophobic cavity. Using a multifaceted set of computational analyses that involve CcO embedded in either an implicit or explicit treatment of lipid membrane, we show that neither Glu-286 nor active-site water likely constitutes the gating element. Detailed energetic and structural analyses of the simulation results indicate that the gating-relevant properties of these structural motifs observed in previous work are likely a result of the simplified computational models employed in those studies.
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Affiliation(s)
- Shuo Yang
- BACTER Graduate Program, University of Wisconsin, Madison, Wisconsin, USA
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