51
|
Titantah JT, Karttunen M. Long-Time Correlations and Hydrophobe-Modified Hydrogen-Bonding Dynamics in Hydrophobic Hydration. J Am Chem Soc 2012; 134:9362-8. [DOI: 10.1021/ja301908a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- John Tatini Titantah
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario,
Canada N6A 5B7
| | - Mikko Karttunen
- Department
of Chemistry, University of Waterloo, 200
University Avenue West,
Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|
52
|
VandeVondele J, Tröster P, Tavan P, Mathias G. Vibrational Spectra of Phosphate Ions in Aqueous Solution Probed by First-Principles Molecular Dynamics. J Phys Chem A 2012; 116:2466-74. [DOI: 10.1021/jp211783z] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Philipp Tröster
- Lehrstuhl für
Biomolekulare
Optik, Ludwig-Maximilians-Universität München
| | - Paul Tavan
- Lehrstuhl für
Biomolekulare
Optik, Ludwig-Maximilians-Universität München
| | - Gerald Mathias
- Lehrstuhl für
Biomolekulare
Optik, Ludwig-Maximilians-Universität München
| |
Collapse
|
53
|
Park SY, Jang DJ. Excited-state hydrogen relay along a blended-alcohol chain as a model system of a proton wire: deuterium effect on the reaction dynamics. Phys Chem Chem Phys 2012; 14:8885-91. [DOI: 10.1039/c2cp23615j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
54
|
Lim H, Jeong H, Park SY, Lee JY, Jang DJ. Excited-state proton-relay dynamics of 7-hydroxyquinoline controlled by solvent reorganization in room temperature ionic liquids. Phys Chem Chem Phys 2012; 14:218-24. [DOI: 10.1039/c1cp22329a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
55
|
Mathias G, Ivanov SD, Witt A, Baer MD, Marx D. Infrared Spectroscopy of Fluxional Molecules from (ab Initio) Molecular Dynamics: Resolving Large-Amplitude Motion, Multiple Conformations, and Permutational Symmetries. J Chem Theory Comput 2011; 8:224-34. [DOI: 10.1021/ct2006665] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gerald Mathias
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Sergei D. Ivanov
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Alexander Witt
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Marcel D. Baer
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| |
Collapse
|
56
|
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]
|
57
|
Clair ECS, Ogren JI, Mamaev S, Kralj JM, Rothschild KJ. Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks. J Biol Phys 2011; 38:153-68. [PMID: 23277676 DOI: 10.1007/s10867-011-9246-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 10/25/2011] [Indexed: 11/30/2022] Open
Abstract
Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm( - 1), which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogen-bonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm( - 1) assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.
Collapse
Affiliation(s)
- Erica C Saint Clair
- Department of Physics, Photonics Center and Molecular Biophysics Laboratory, Boston University, Boston, MA 02215 USA
| | | | | | | | | |
Collapse
|
58
|
Goyal P, Ghosh N, Phatak P, Clemens M, Gaus M, Elstner M, Cui Q. Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra. J Am Chem Soc 2011; 133:14981-97. [PMID: 21761868 PMCID: PMC3178665 DOI: 10.1021/ja201568s] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as the PRG would require the protein to raise the pK(a) of a hydronium by almost 11 pK(a) units, which is difficult considering known cases of pK(a) shifts in proteins. Our recent quantum mechanics/molecular mechanics (QM/MM) simulations suggested an alternative "intermolecular proton bond" model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pK(a) values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting X-ray structure, and nuclear quantum effects, the "intermolecular proton bond" model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the "intermolecular proton bond" model is likely applicable to the PRG in biomolecular proton pumps in general.
Collapse
Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| | - Nilanjan Ghosh
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| | - Prasad Phatak
- Department of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straβe 10, D-38106 Braunschweig, Germany
| | - Maike Clemens
- Department of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straβe 10, D-38106 Braunschweig, Germany
| | - Michael Gaus
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straβe 10, D-38106 Braunschweig, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| |
Collapse
|
59
|
Hendler RW, Meuse CW, Braiman MS, Smith PD, Kakareka JW. Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates. APPLIED SPECTROSCOPY 2011; 65:1029-45. [PMID: 21929858 PMCID: PMC4167422 DOI: 10.1366/11-06302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its M(F) and M(S) components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm(-1) for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the M(F) pathway of the parallel cycles model of the photocycle.
Collapse
Affiliation(s)
- Richard W. Hendler
- Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
- Biochemical Sciences Division, National Institute of Standards and Technology, Gaithersburg. Maryland 20899
| | - Curtis W. Meuse
- Biochemical Sciences Division, National Institute of Standards and Technology, Gaithersburg. Maryland 20899
| | - Mark S. Braiman
- Syracuse University Chemistry Department, Syracuse NY 13244-4100
| | - Paul D. Smith
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892
| | - John W. Kakareka
- Division of Computational Biosciences, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892
| |
Collapse
|
60
|
Proton transfer via a transient linear water-molecule chain in a membrane protein. Proc Natl Acad Sci U S A 2011; 108:11435-9. [PMID: 21709261 DOI: 10.1073/pnas.1104735108] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-resolution protein ground-state structures of proton pumps and channels have revealed internal protein-bound water molecules. Their possible active involvement in protein function has recently come into focus. An illustration of the formation of a protonated protein-bound water cluster that is actively involved in proton transfer was described for the membrane protein bacteriorhodopsin (bR) [Garczarek F, Gerwert K (2006) Nature 439:109-112]. Here we show through a combination of time-resolved FTIR spectroscopy and molecular dynamics simulations that three protein-bound water molecules are rearranged by a protein conformational change that resulted in a transient Grotthuss-type proton-transfer chain extending through a hydrophobic protein region of bR. This transient linear water chain facilitates proton transfer at an intermediate conformation only, thereby directing proton transfer within the protein. The rearrangement of protein-bound water molecules that we describe, from inactive positions in the ground state to an active chain in an intermediate state, appears to be energetically favored relative to transient incorporation of water molecules from the bulk. Our discovery provides insight into proton-transfer mechanisms through hydrophobic core regions of ubiquitous membrane spanning proteins such as G-protein coupled receptors or cytochrome C oxidases.
Collapse
|
61
|
Mathias G, Baer MD. Generalized Normal Coordinates for the Vibrational Analysis of Molecular Dynamics Simulations. J Chem Theory Comput 2011; 7:2028-39. [DOI: 10.1021/ct2001304] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gerald Mathias
- Lehrstuhl für BioMolekulare Optik, Ludwig−Maximilians Universität München, Oettingenstrasse 67, 80538 München, Germany
| | - Marcel D. Baer
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| |
Collapse
|
62
|
Lórenz-Fonfría VA, Kandori H, Padrós E. Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle. J Phys Chem B 2011; 115:7972-85. [PMID: 21615095 DOI: 10.1021/jp201739w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.
Collapse
Affiliation(s)
- Víctor A Lórenz-Fonfría
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona 08193, Spain.
| | | | | |
Collapse
|
63
|
Park SY, Jeong H, Jang DJ. Anomalously Slow Proton Transport of a Water Molecule. J Phys Chem B 2011; 115:6023-31. [DOI: 10.1021/jp112210x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sun-Young Park
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| | - Hyeok Jeong
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| | - Du-Jeon Jang
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| |
Collapse
|
64
|
Baer M, Marx D, Mathias G. Assigning Predissociation Infrared Spectra of Microsolvated Hydronium Cations H3O+⋅(H2)n (n=0, 1, 2, 3) by Ab Initio Molecular Dynamics. Chemphyschem 2011; 12:1906-15. [DOI: 10.1002/cphc.201000955] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/02/2011] [Indexed: 11/07/2022]
|
65
|
Wolf S, Freier E, Potschies M, Hofmann E, Gerwert K. Directional proton transfer in membrane proteins achieved through protonated protein-bound water molecules: a proton diode. Angew Chem Int Ed Engl 2011; 49:6889-93. [PMID: 20680951 DOI: 10.1002/anie.201001243] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Steffen Wolf
- Lehrstuhl für Biophysik, Ruhr-University Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | | | | | | | | |
Collapse
|
66
|
Radu I, Schleeger M, Nack M, Heberle J. Time-resolved FT-IR Spectroscopy of Membrane Proteins. Aust J Chem 2011. [DOI: 10.1071/ch10286] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Time-resolved Fourier transform infrared spectroscopy (FT-IR) offers distinct advantages concerning restrictions pertinent to biomolecules. In particular, it is possible to monitor the temporal evolution of the reaction mechanism of complex machineries as membrane proteins, where other techniques encounter significant experimental difficulties. Here, we present the classical principles and experimental realizations of time-resolved FT-IR spectroscopy together with recent developments employed in our laboratory. Examples from applications to retinal proteins are reviewed that underline the impact of time-resolved FT-IR spectroscopy on the understanding of protein reactions on the level of single bonds.
Collapse
|
67
|
Lankau T, Yu CH. A quantum description of the proton movement in an idealized NHN+ bridge. Phys Chem Chem Phys 2011; 13:12758-69. [DOI: 10.1039/c0cp02172e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
68
|
Park SY, Lee YS, Jang DJ. Ground-state proton-transfer dynamics governed by configurational optimization. Phys Chem Chem Phys 2011; 13:3730-6. [DOI: 10.1039/c0cp01977a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
69
|
Fiethen SA, Staemmler V, Nair NN, Ribas-Arino J, Schreiner E, Marx D. Revealing the magnetostructural dynamics of [2Fe-2S] ferredoxins from reduced-dimensionality analysis of antiferromagnetic exchange coupling fluctuations. J Phys Chem B 2010; 114:11612-9. [PMID: 20718446 DOI: 10.1021/jp1014912] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metalloproteins are biomolecular hybrids composed of an "inorganic core" embedded in a "bioorganic matrix". Cofactors typically contain transition metal clusters with complex electronic structure whereas the protein host undergoes dynamics on many length and time scales. This renders computational studies of spectroscopic properties challenging, in particular, when magnetic interactions are involved. In the present study we introduce a simplified description of the antiferromagnetic exchange coupling J in reduced dimensionality which allows one to study magnetostructural dynamics of [2Fe-2S] type iron-sulfur proteins in their oxidized form by molecular dynamics. It is demonstrated that parametrization in terms of a 2D J-surface faithfully reproduces the rigorous results both in vacuo and in Anabaena ferredoxin. In particular, we present a parametrization which relies on a spin-projected density functional approach based on two Kohn-Sham determinants corrected for self-interaction via a self-consistent linear-response Hubbard-U technique. This yields an average J for Anabaena Fd in close agreement with experimental in vitro results without any specific adjustment or fitting. The analytical J-surface can be used for [2Fe-2S] proteins in their oxidized form in general and the idea can be extended to other metalloproteins as well as to other spectroscopic properties.
Collapse
Affiliation(s)
- S Annamaria Fiethen
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | | | | | | | | | | |
Collapse
|
70
|
Sudo Y, Ihara K, Kobayashi S, Suzuki D, Irieda H, Kikukawa T, Kandori H, Homma M. A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties. J Biol Chem 2010; 286:5967-76. [PMID: 21135094 DOI: 10.1074/jbc.m110.190058] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Rhodopsins possess retinal chromophore surrounded by seven transmembrane α-helices, are widespread in prokaryotes and in eukaryotes, and can be utilized as optogenetic tools. Although rhodopsins work as distinctly different photoreceptors in various organisms, they can be roughly divided according to their two basic functions, light-energy conversion and light-signal transduction. In microbes, light-driven proton transporters functioning as light-energy converters have been modified by evolution to produce sensory receptors that relay signals to transducer proteins to control motility. In this study, we cloned and characterized two newly identified microbial rhodopsins from Haloquadratum walsbyi. One of them has photochemical properties and a proton pumping activity similar to the well known proton pump bacteriorhodopsin (BR). The other, named middle rhodopsin (MR), is evolutionarily transitional between BR and the phototactic sensory rhodopsin II (SRII), having an SRII-like absorption maximum, a BR-like photocycle, and a unique retinal composition. The wild-type MR does not have a light-induced proton pumping activity. On the other hand, a mutant MR with two key hydrogen-bonding residues located at the interaction surface with the transducer protein HtrII shows robust phototaxis responses similar to SRII, indicating that MR is potentially capable of the signaling. These results demonstrate that color tuning and insertion of the critical threonine residue occurred early in the evolution of sensory rhodopsins. MR may be a missing link in the evolution from type 1 rhodopsins (microorganisms) to type 2 rhodopsins (animals), because it is the first microbial rhodopsin known to have 11-cis-retinal similar to type 2 rhodopsins.
Collapse
Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
71
|
Sun J, Bousquet D, Forbert H, Marx D. Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 2010; 133:114508. [DOI: 10.1063/1.3481576] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
72
|
Baer M, Marx D, Mathias G. Theoretische Botenspektroskopie von mikrosolvatisierten Hydronium- und Zundel-Kationen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
73
|
Baer M, Marx D, Mathias G. Theoretical Messenger Spectroscopy of Microsolvated Hydronium and Zundel Cations. Angew Chem Int Ed Engl 2010; 49:7346-9. [DOI: 10.1002/anie.201001672] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
74
|
Wolf S, Freier E, Potschies M, Hofmann E, Gerwert K. Gerichteter Protonentransfer in Membranproteinen mittels protonierter proteingebundener Wassermoleküle: eine Protonendiode. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
75
|
Thomas V, Maurer P, Iftimie R. On the Formation of Proton-Shared and Contact Ion Pair Forms during the Dissociation of Moderately Strong Acids: An Ab Initio Molecular Dynamics Investigation. J Phys Chem B 2010; 114:8147-55. [DOI: 10.1021/jp102822c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vibin Thomas
- Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal, H3C3J7, Canada
| | - Patrick Maurer
- Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal, H3C3J7, Canada
| | - Radu Iftimie
- Département de Chimie, Université de Montréal,CP 6128, succursale Centre-Ville, Montréal, H3C3J7, Canada
| |
Collapse
|
76
|
Dopieralski PD, Latajka Z, Olovsson I. Proton Transfer Dynamics in Crystalline Maleic Acid from Molecular Dynamics Calculations. J Chem Theory Comput 2010; 6:1455-61. [DOI: 10.1021/ct100078w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Przemyslaw D. Dopieralski
- University of Wroclaw, Faculty of Chemistry, 14 Joliot-Curie Str. 50-383 Wroclaw, Poland, and Department of Materials Chemistry, Ångström Laboratory, SE-751 21 Uppsala, Sweden
| | - Zdzislaw Latajka
- University of Wroclaw, Faculty of Chemistry, 14 Joliot-Curie Str. 50-383 Wroclaw, Poland, and Department of Materials Chemistry, Ångström Laboratory, SE-751 21 Uppsala, Sweden
| | - Ivar Olovsson
- University of Wroclaw, Faculty of Chemistry, 14 Joliot-Curie Str. 50-383 Wroclaw, Poland, and Department of Materials Chemistry, Ångström Laboratory, SE-751 21 Uppsala, Sweden
| |
Collapse
|
77
|
Jun B, Kim S. Real-time structural transitions are coupled to chemical steps in ATP hydrolysis by Eg5 kinesin. J Biol Chem 2010; 285:11073-7. [PMID: 20154092 PMCID: PMC2856982 DOI: 10.1074/jbc.c110.103762] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/08/2010] [Indexed: 11/06/2022] Open
Abstract
At the biochemical level, motor proteins are enzymatic molecules that function by converting chemical energy into mechanical motion. The key element for energy transduction and a major unresolved question common for all motor proteins is the coordination between the chemical and conformational steps in ATP hydrolysis. Here we show time-lapse monitoring of an in vitro ATP hydrolysis reaction by the motor domain of a human Kinesin-5 protein (Eg5) using difference Fourier transform infrared spectroscopy and UV photolysis of caged ATP. In this first continuous observation of a biological reaction coordinate from substrate to product, direct spectral markers for two catalytic events are measured: proton abstraction from nucleophilic water by the catalytic base and formation of the inorganic phosphate leaving group. Simultaneous examination of conformational switching in Eg5, in parallel with catalytic steps, shows structural transitions in solution consistent with published crystal structures of the prehydrolytic and ADP-bound states. In addition, we detect structural modifications in the Eg5 motor domain during bond cleavage between the beta- and gamma-phosphates of ATP. This conclusion challenges mechanochemical models for motor proteins that utilize only two stages of the catalytic cycle to drive force and motion.
Collapse
Affiliation(s)
- Bokkyoo Jun
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112
| | - Sunyoung Kim
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112
| |
Collapse
|
78
|
Ghosh N, Prat-Resina X, Gunner MR, Cui Q. Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model. Biochemistry 2010; 48:2468-85. [PMID: 19243111 DOI: 10.1021/bi8021284] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As stringent tests for the molecular model and computational protocol, microscopic pK(a) calculations are performed for the key residue, Glu286, in cytochrome c oxidase (CcO) using a combined quantum mechanical/molecular mechanical (QM/MM) potential and a thermodynamic integration protocol. The impact of the number of water molecules in the hydrophobic cavity and protonation state of several key residues (e.g., His334, Cu(B)-bound water, and PRD(a3)) on the computed microscopic pK(a) values of Glu286 has been systematically examined. To help evaluate the systematic errors in the QM/MM-based protocol, microscopic pK(a) calculations have also been carried out for sites in a soluble protein (Asp70 in T4 lysozyme) and a better-characterized membrane protein (Asp85 in bacteriorhodopsin). Overall, the results show a significant degree of internal consistency and reproducibility that support the effectiveness of the computational framework. Although the number of water molecules in the hydrophobic cavity does not greatly influence the computed pK(a) of Glu286, the protonation states of several residues, some of which are rather far away, have more significant impacts. Adopting the standard protonation state for all titratable residues leaves a large net charge on the system and a significantly elevated pK(a) for Glu286, highlighting that any attempt to address the energetics of proton transfers in CcO at a microscopic level should carefully select the protonation state of residues, even those not in the immediate neighborhood of the active site. The calculations indirectly argue against the deprotonation of His334 for the proton pumping process, although further studies that explicitly compute its pK(a) are required for a more conclusive statement. Finally, the deprotonated Glu286 is found to be in a stable water-mediated connection with PRD(a3) for at least several nanoseconds when this presumed pumping site is protonated. This does not support the proposed role of Glu286 as a robust gating valve that prevents proton leakage, although a conclusive statement awaits a more elaborate characterization of the Glu286-PRD(a3) connectivity with free energy simulations and a protonated PRD(a3). The large sets of microscopic simulations performed here have provided useful guidance to the establishment of a meaningful molecular model and effective computational protocol for explicitly analyzing the proton transfer kinetics in CcO, which is required for answering key questions regarding the pumping function of this fascinating and complex system.
Collapse
Affiliation(s)
- Nilanjan Ghosh
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|
79
|
Orban T, Gupta S, Palczewski K, Chance MR. Visualizing water molecules in transmembrane proteins using radiolytic labeling methods. Biochemistry 2010; 49:827-34. [PMID: 20047303 DOI: 10.1021/bi901889t] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often colocalize with strategically placed polar or charged groups critical for protein function, yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of "ordered" waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern, and thus, the observed waters likely represent a subset of tightly bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, because of advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins.
Collapse
Affiliation(s)
- Tivadar Orban
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA
| | | | | | | |
Collapse
|
80
|
Stoyanov ES, Stoyanova IV, Tham FS, Reed CA. H(aq)+ structures in proton wires inside nanotubes. J Am Chem Soc 2010; 131:17540-1. [PMID: 19911820 DOI: 10.1021/ja907708g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrated carborane acid H(CHB(11)I(11)).8H(2)O crystallizes in nanometer-diameter tubes of H(aq)(+) enclosed by walls of carborane anions. Three different types of H(aq)(+) clusters are found in these tubes: a symmetrical H(13)O(6)(+) ion with an unusually elongated Zundel-type H(5)O(2)(+) core, two hydrated H(7)O(3)(+) ions, and an unprecedented H(17)O(8)(+) ion having a nearly square core. All of the H(aq)(+) cations show unexpectedly longer O...O separations than in discrete H(aq)(+) ions, indicating greater delocalization of positive charge. The centrosymmetric H(aq)(+) ions are linked via short H bonds, forming a true one-dimensional proton wire.
Collapse
Affiliation(s)
- Evgenii S Stoyanov
- Department of Chemistry, University of California, Riverside, California 92521-0403, USA.
| | | | | | | |
Collapse
|
81
|
Dopieralski PD, Latajka Z, Olovsson I. Proton-transfer dynamics in the (HCO3
−)2 dimer of KHCO3 from Car–Parrinello and path-integrals molecular dynamics calculations. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2010; 66:222-8. [DOI: 10.1107/s0108768110002314] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 01/18/2010] [Indexed: 11/10/2022]
Abstract
The proton motion in the (HCO_3^-)2 dimer of KHCO3 at 298 K has been studied with Car–Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298 K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1 fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20 fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations.
Collapse
|
82
|
Sajadi M, Ajaj Y, Ioffe I, Weingärtner H, Ernsting N. Terahertz Absorption Spectroscopy of a Liquid Using a Polarity Probe: A Case Study of Trehalose/Water Mixtures. Angew Chem Int Ed Engl 2010; 49:454-7. [DOI: 10.1002/anie.200904997] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mohsen Sajadi
- Department of Chemistry, Humboldt University, Brook‐Taylor‐Strasse 2, 12489 Berlin(Germany)
| | - Yathrib Ajaj
- Physical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstrasse 150 44780 Bochum (Germany)
| | - Ilya Ioffe
- Department of Chemistry, Humboldt University, Brook‐Taylor‐Strasse 2, 12489 Berlin(Germany)
| | - Hermann Weingärtner
- Physical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstrasse 150 44780 Bochum (Germany)
| | - Nikolaus P. Ernsting
- Department of Chemistry, Humboldt University, Brook‐Taylor‐Strasse 2, 12489 Berlin(Germany)
| |
Collapse
|
83
|
Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
84
|
Yan YA, Kühn O. Geometric correlations and infrared spectrum of adenine–uracil hydrogen bonds in CDCl3 solution. Phys Chem Chem Phys 2010; 12:15695-703. [DOI: 10.1039/c0cp00009d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
85
|
Sajadi M, Ajaj Y, Ioffe I, Weingärtner H, Ernsting N. Terahertz‐Absorptionsspektroskopie einer Flüssigkeit mithilfe einer Polaritätssonde: Anwendung auf Trehalose‐Wasser‐Mischungen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mohsen Sajadi
- Institut für Chemie, Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
| | - Yathrib Ajaj
- Lehrstuhl II, Fakultät für Chemie und Biochemie, Ruhr‐Universität Bochum, Universitätsstraße 150, 44780 Bochum (Deutschland)
| | - Ilya Ioffe
- Institut für Chemie, Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
| | - Hermann Weingärtner
- Lehrstuhl II, Fakultät für Chemie und Biochemie, Ruhr‐Universität Bochum, Universitätsstraße 150, 44780 Bochum (Deutschland)
| | - Nikolaus P. Ernsting
- Institut für Chemie, Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
| |
Collapse
|
86
|
Park SY, Jang DJ. Accumulated Proton-Donating Ability of Solvent Molecules in Proton Transfer. J Am Chem Soc 2009; 132:297-302. [DOI: 10.1021/ja907491u] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sun-Young Park
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| | - Du-Jeon Jang
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| |
Collapse
|
87
|
Prakash M, Subramanian V, Gadre SR. Stepwise Hydration of Protonated Carbonic Acid: A Theoretical Study. J Phys Chem A 2009; 113:12260-75. [DOI: 10.1021/jp904576u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Prakash
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| | - Shridhar R. Gadre
- Chemical Laboratory, Central Leather Research Institute, Central Leather Research Institute, Adyar, Chennai 600 020, India, and Department of Chemistry, University of Pune, Pune 411 007, India
| |
Collapse
|
88
|
Vendrell O, Gatti F, Meyer HD. Full dimensional (15 dimensional) quantum-dynamical simulation of the protonated water-dimer IV: Isotope effects in the infrared spectra of D(D2O)2+, H(D2O)2+, and D(H2O)2+ isotopologues. J Chem Phys 2009; 131:034308. [DOI: 10.1063/1.3183166] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
89
|
Altarsha M, Wang D, Benighaus T, Kumar D, Thiel W. QM/MM Study of the Second Proton Transfer in the Catalytic Cycle of the D251N Mutant of Cytochrome P450cam. J Phys Chem B 2009; 113:9577-88. [DOI: 10.1021/jp809838k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Muhannad Altarsha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Dongqi Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Tobias Benighaus
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Devesh Kumar
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
90
|
Phatak P, Frähmcke JS, Wanko M, Hoffmann M, Strodel P, Smith J, Suhai S, Bondar AN, Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc 2009; 131:7064-78. [PMID: 19405533 PMCID: PMC2746972 DOI: 10.1021/ja809767v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.
Collapse
Affiliation(s)
- Prasad Phatak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Jan S. Frähmcke
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Marius Wanko
- BCCMS, Universität Bremen, D-28334 Bremen, Germany
| | | | - Paul Strodel
- Accelrys Ltd., Cambridge CB4 0WN, United Kingdom
| | - Jeremy Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Center for Molecular Biophysics, Oak Ridge National Laboratory, PO BOX 2008 MS6164, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Ave, Knoxville Tennessee 37996, USA
| | - Sándor Suhai
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
| | - Ana-Nicoleta Bondar
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Med. Sci. I, D-347, Irvine, CA 92697, USA
| | - Marcus Elstner
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
| |
Collapse
|
91
|
Lórenz-Fonfría VA, Kandori H. Spectroscopic and Kinetic Evidence on How Bacteriorhodopsin Accomplishes Vectorial Proton Transport under Functional Conditions. J Am Chem Soc 2009; 131:5891-901. [DOI: 10.1021/ja900334c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Víctor A. Lórenz-Fonfría
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| |
Collapse
|
92
|
Bergo VB, Spudich EN, Spudich JL, Rothschild KJ. Active water in protein-protein communication within the membrane: the case of SRII-HtrII signal relay. Biochemistry 2009; 48:811-3. [PMID: 19187030 DOI: 10.1021/bi802180a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We detect internal water molecules in a membrane-embedded receptor-transducer complex and demonstrate water structure changes during formation of the signaling state. Time-resolved FTIR spectroscopy reveals stimulus-induced repositioning of one or more structurally active water molecules to a significantly more hydrophobic environment in the signaling state of the sensory rhodopsin II (SRII)-transducer (HtrII) complex. These waters, distinct from bound water molecules within the SRII receptor, appear to be in the middle of the transmembrane interface region near the Tyr199(SRII)-Asn74(HtrII) hydrogen bond. We conclude that water potentially plays an important role in the SRII --> HtrII signal transfer mechanism in the membrane's hydrophobic core.
Collapse
Affiliation(s)
- Vladislav B Bergo
- Department of Physics, Molecular Biophysics Laboratory, and Center for Photonics, Boston University, Boston, Massachusetts 02215, USA
| | | | | | | |
Collapse
|
93
|
Wassenaar TA, Daura X, Padrós E, Mark AE. Calcium binding to the purple membrane: A molecular dynamics study. Proteins 2009; 74:669-81. [PMID: 18704943 DOI: 10.1002/prot.22182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca(2+) near the Schiff base and another one near the Glu194-Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations.
Collapse
Affiliation(s)
- Tsjerk A Wassenaar
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | | | | | | |
Collapse
|
94
|
Thirumuruganandham SP, Urbassek HM. Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. J Mol Model 2009; 15:959-69. [DOI: 10.1007/s00894-008-0446-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 12/23/2008] [Indexed: 11/25/2022]
|
95
|
Wolf S, Freier E, Gerwert K. How does a membrane protein achieve a vectorial proton transfer via water molecules? Chemphyschem 2009; 9:2772-8. [PMID: 19072873 DOI: 10.1002/cphc.200800703] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present a detailed mechanism for the proton transfer from a protein-bound protonated water cluster to the bulk water directed by protein side chains in the membrane protein bacteriorhodopsin. We use a combined approach of time-resolved Fourier transform infrared spectroscopy, molecular dynamics simulations, and X-ray structure analysis to elucidate the functional role of a hydrogen bond between Ser193 and Glu204. These two residues seal the internal protonated water cluster from the bulk water and the protein surface. During the photocycle of bacteriorhodopsin, a transient protonation of Glu204 leads to a breaking of this hydrogen bond. This breaking opens the gate to the extracellular bulk water, leading to a subsequent proton release from the protonated water cluster. We show in detail how the protein achieves vectorial proton transfer via protonated water clusters in contrast to random proton transfer in liquid water.
Collapse
Affiliation(s)
- Steffen Wolf
- Department of Biophysics, ND 04 North, Ruhr-University BochumD-44780 Bochum, Germany
| | | | | |
Collapse
|
96
|
Baer M, Mathias G, Kuo IFW, Tobias DJ, Mundy CJ, Marx D. Spectral signatures of the pentagonal water cluster in bacteriorhodopsin. Chemphyschem 2009; 9:2703-7. [PMID: 19025752 DOI: 10.1002/cphc.200800473] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marcel Baer
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | | | | | | | | | | |
Collapse
|
97
|
Abstract
The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton-transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen-bonded networks, which may include internal water molecules. The terminal step of the proton-transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton-release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen-bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.
Collapse
Affiliation(s)
- Alain Chaumont
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | | | | | | |
Collapse
|
98
|
Radu I, Schleeger M, Bolwien C, Heberle J. Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins. Photochem Photobiol Sci 2009; 8:1517-28. [DOI: 10.1039/b9pp00050j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
99
|
Hyeon-Deuk K, Ando K. Semiquantum molecular dynamics simulation of liquid water by time-dependent Hartree approach. J Chem Phys 2009; 131:064501. [DOI: 10.1063/1.3200937] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
100
|
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A 2008; 105:19672-7. [PMID: 19064907 DOI: 10.1073/pnas.0810712105] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The positions of protons are not available in most high-resolution structural data of biomolecules, thus the identity of proton storage sites in biomolecules that transport proton is generally difficult to determine unambiguously. Using combined quantum mechanical/molecular mechanical computations, we demonstrate that a pair of conserved glutamate residues (Glu 194/204) bonded by a delocalized proton is the proton release group that has been long sought in the proton pump, bacteriorhodopsin. This model is consistent with all available experimental structural and infrared data for both the wild-type bacteriorhodopsin and several mutants. In particular, the continuum infrared band in the 1,800- to 2,000-cm(-1) region is shown to arise due to the partially delocalized nature of the proton between the glutamates in the wild-type bacteriorhodopsin; alternations in the flexibility of the glutamates and electrostatic nature of nearby residues in various mutants modulate the degree of proton delocalization and therefore intensity of the continuum band. The strong hydrogen bond between Glu 194/204 also significantly shifts the carboxylate stretches of these residues well <1,700 cm(-1), which explains why carboxylate spectral shift was not observed experimentally in the typical >1,700-cm(-1) region upon proton release. By contrast, simulations with the proton restrained on the nearby water cluster, as proposed by several recent studies [see, for example, Garezarek K, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439:109], led to significant structural deviations from available X-ray structures. This study establishes a biological function for strong, low-barrier hydrogen bonds.
Collapse
|