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Selikhanov G, Fufina T, Guenther S, Meents A, Gabdulkhakov A, Vasilieva L. X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. IUCRJ 2022; 9:261-271. [PMID: 35371503 PMCID: PMC8895020 DOI: 10.1107/s2052252521013178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
The first steps of the global process of photosynthesis take place in specialized membrane pigment-protein complexes called photosynthetic reaction centers (RCs). The RC of the photosynthetic purple bacterium Rhodobacter sphaeroides, a relatively simple analog of the more complexly organized photosystem II in plants, algae and cyanobacteria, serves as a convenient model for studying pigment-protein interactions that affect photochemical processes. In bacterial RCs the bacteriochlorophyll (BChl) dimer P serves as the primary electron donor, and its redox potential is a critical factor in the efficient functioning of the RC. It has previously been shown that the replacement of Phe M197 by His strongly affects the oxidation potential of P (E m P/P+), increasing its value by 125 mV, as well as increasing the thermal stability of RC and its stability in response to external pressure. The crystal structures of F(M197)H RC at high resolution obtained using various techniques presented in this report clarify the optical and electrochemical properties of the primary electron donor and the increased resistance of the mutant complex to denaturation. The electron-density maps are consistent with the donation of a hydrogen bond from the imidazole group of His M197 to the C2-acetyl carbonyl group of BChl PB. The formation of this hydrogen bond leads to a considerable out-of-plane rotation of the acetyl carbonyl group and results in a 1.2 Å shift of the O atom of this group relative to the wild-type structure. Besides, the distance between BChl PA and PB in the area of pyrrole ring I was found to be increased by up to 0.17 Å. These structural changes are discussed in association with the spectral properties of BChl dimer P. The electron-density maps strongly suggest that the imidazole group of His M197 accepts another hydrogen bond from the nearest water molecule, which in turn appears to form two more hydrogen bonds to Asn M195 and Asp L155. As a result of the F(M197)H mutation, BChl PB finds itself connected to the extensive hydrogen-bonding network that pre-existed in wild-type RC. Dissimilarities in the two hydrogen-bonding networks near the M197 and L168 sites may account for the different changes of the E m P/P+ in F(M197)H and H(L168)F RCs. The involvement of His M197 in the hydrogen-bonding network also appears to be related to stabilization of the F(M197)H RC structure. Analysis of the experimental data presented here and of the data available in the literature points to the fact that the hydrogen-bonding networks in the vicinity of BChl dimer P may play an important role in fine-tuning the redox properties of the primary electron donor.
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Affiliation(s)
- Georgii Selikhanov
- Group of Structural Studies of Macromolecular Complexes, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
| | - Tatiana Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
| | - Sebastian Guenther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Azat Gabdulkhakov
- Group of Structural Studies of Macromolecular Complexes, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Pushchino 142290, Moscow Region, Russian Federation
| | - Lyudmila Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, Pushchino 142290, Moscow Region, Russian Federation
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2
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Schauperl M, Podewitz M, Waldner BJ, Liedl KR. Enthalpic and Entropic Contributions to Hydrophobicity. J Chem Theory Comput 2016; 12:4600-10. [PMID: 27442443 PMCID: PMC5024328 DOI: 10.1021/acs.jctc.6b00422] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrophobic hydration plays a key role in a vast variety of biological processes, ranging from the formation of cells to protein folding and ligand binding. Hydrophobicity scales simplify the complex process of hydration by assigning a value describing the averaged hydrophobic character to each amino acid. Previously published scales were not able to calculate the enthalpic and entropic contributions to the hydrophobicity directly. We present a new method, based on Molecular Dynamics simulations and Grid Inhomogeneous Solvation Theory, that calculates hydrophobicity from enthalpic and entropic contributions. Instead of deriving these quantities from the temperature dependence of the free energy of hydration or as residual of the free energy and the enthalpy, we directly obtain these values from the phase space occupied by water molecules. Additionally, our method is able to identify regions with specific enthalpic and entropic properties, allowing to identify so-called "unhappy water" molecules, which are characterized by weak enthalpic interactions and unfavorable entropic constraints.
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Affiliation(s)
- Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
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3
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di Cocco ME, Bianchetti C, Chiellini F. 1H NMR Studies of Alginate Interactions with Amino Acids. J BIOACT COMPAT POL 2016. [DOI: 10.1177/088391103037015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The interactions between alginate and the amino acids, histidine, lysine, phenylalanine, and alanine, were studied by Proton Nuclear Magnetic Resonance. The characterization of the amino acids interaction with alginate was performed by 1D and 2D-NOESY experiments. Measurements of 1H NMR nonselective and selective relaxation rates in the absence and presence of alginate were used to calculate interaction constants between each amino acid and alginate. The interaction constants were found to be related to the hydrophobicity of the different amino acid side-chains. The interaction constant between phenylalanine and Ca2+ crosslinked alginate was also determined. There was no apparent differences observed in the crosslinked and the solution amino acid-alginate interactions. On the basis of the experimental results obtained, a model of the interaction between amino acids and alginate was proposed.
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Affiliation(s)
- Maria Enrica di Cocco
- Department of Chemistry, University ‘‘La Sapienza’’, Piazzale Aldo Moro, 5 - 00185 Roma, Italy,
| | - Cristiano Bianchetti
- Department of Chemistry, University ‘‘La Sapienza’’, Piazzale Aldo Moro, 5 - 00185 Roma, Italy
| | - Federica Chiellini
- Department of Chemistry & Industrial Chemistry, University of Pisa, Via Risorgimento, 35 - 56126 Pisa, Italy
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Nishizawa K, Nishizawa M, Gnanasambandam R, Sachs F, Sukharev SI, Suchyna TM. Effects of Lys to Glu mutations in GsMTx4 on membrane binding, peptide orientation, and self-association propensity, as analyzed by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2767-78. [PMID: 26342676 DOI: 10.1016/j.bbamem.2015.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
Abstract
GsMTx4, a gating modifier peptide acting on cationic mechanosensitive channels, has a positive charge (+5e) due to six Lys residues. The peptide does not have a stereospecific binding site on the channel but acts from the boundary lipids within a Debye length of the pore probably by changing local stress. To gain insight into how these Lys residues interact with membranes, we performed molecular dynamics simulations of Lys to Glu mutants in parallel with our experimental work. In silico, K15E had higher affinity for 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine bilayers than wild-type (WT) peptide or any other mutant tested, and showed deeper penetration than WT, a finding consistent with the experimental data. Experimentally, the inhibitory activities of K15E and K25E were most compromised, whereas K8E and K28E inhibitory activities remained similar to WT peptide. Binding of WT in an interfacial mode did not influence membrane thickness. With interfacial binding, the direction of the dipole moments of K15E and K25E was predicted to differ from WT, whereas those of K8E and K28E oriented similarly to that of WT. These results support a model in which binding of GsMTx4 to the membrane acts like an immersible wedge that serves as a membrane expansion buffer reducing local stress and thus inhibiting channel activity. In simulations, membrane-bound WT attracted other WT peptides to form aggregates. This may account for the positive cooperativity observed in the ion channel experiments. The Lys residues seem to fine-tune the depth of membrane binding, the tilt angle, and the dipole moments.
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Affiliation(s)
| | | | | | - Frederick Sachs
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Sergei I Sukharev
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas M Suchyna
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
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5
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Fufina TY, Vasilieva LG, Gabdulkhakov AG, Shuvalov VA. The L(M196)H mutation in Rhodobacter sphaeroides reaction center results in new electrostatic interactions. PHOTOSYNTHESIS RESEARCH 2015; 125:23-29. [PMID: 25480338 DOI: 10.1007/s11120-014-0062-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
New histidine residue was introduced in M196 position in the reaction center of Rhodobacter sphaeroides in order to alter polarity of the BChl dimer's protein environment and to study how it affects properties and structure of the primary electron donor P. It was shown that in the absorption spectrum of the mutant RC the 6 nm red shift of the Q Y P band was observed together with considerable decrease of its amplitude. The mid-point potential of P/P (+) in the mutant RC was increased by +65 (±15) mV as compared to the E m P/P (+) value in the wild-type RC suggesting that the mutation resulted in new pigment-protein interactions. Crystal structure of RC L(M196)H determined at 2.4 Å resolution implies that BChl Р В and introduced histidine-M196 organize new electrostatic contact that may be specified either as π-π staking or as hydrogen-π interaction. Besides, the structure of the mutants RC shows that His-M196 apparently became involved in hydrogen bond network existing in BChl Р В vicinity that may favor stability of the mutant RC.
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Affiliation(s)
- Tatiana Y Fufina
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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6
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Angles d’Ortoli T, Sjöberg NA, Vasiljeva P, Lindman J, Widmalm G, Bergenstråhle-Wohlert M, Wohlert J. Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers. J Phys Chem B 2015; 119:9559-70. [DOI: 10.1021/acs.jpcb.5b02866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Thibault Angles d’Ortoli
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Nils A. Sjöberg
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Polina Vasiljeva
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Jonas Lindman
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Malin Bergenstråhle-Wohlert
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg
Wood Science Center, and the Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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7
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Vasilieva LG, Fufina TY, Gabdulkhakov AG, Shuvalov VA. Different effects of identical symmetry-related mutations near the bacteriochlorophyll dimer in the photosynthetic reaction center of Rhodobacter sphaeroides. BIOCHEMISTRY (MOSCOW) 2015; 80:647-53. [DOI: 10.1134/s0006297915060012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Zabelin AA, Shkuropatova VA, Shuvalov VA, Shkuropatov AY. FTIR spectroscopy of the reaction center of Chloroflexus aurantiacus: Photoreduction of the bacteriopheophytin electron acceptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1013-21. [DOI: 10.1016/j.bbabio.2011.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 11/25/2022]
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9
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Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins. Biophys J 2010; 98:470-7. [PMID: 20141761 DOI: 10.1016/j.bpj.2009.10.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 10/21/2009] [Accepted: 10/22/2009] [Indexed: 11/23/2022] Open
Abstract
Born-type electrostatic continuum methods have been an indispensable ingredient in a variety of implicit-solvent methods that reduce computational effort by orders of magnitude compared to explicit-solvent MD simulations and thus enable treatment using larger systems and/or longer times. An analysis of the limitations and failures of the Born approaches serves as a guide for fundamental improvements without diminishing the importance of prior works. One of the major limitations of the Born theory is the lack of a liquidlike description of the response of solvent dipoles to the electrostatic field of the solute and the changes therein, a feature contained in the continuum Langevin-Debye (LD) model applied here to investigate how Coulombic interactions depend on the location of charges relative to the protein/water boundary. This physically more realistic LD model is applied to study the stability of salt bridges. When compared head to head using the same (independently measurable) physical parameters (radii, dielectric constants, etc.), the LD model is in good agreement with observations, whereas the Born model is grossly in error. Our calculations also suggest that a salt bridge on the protein's surface can be stabilizing when the charge separation is < or =4 A.
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10
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Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model. Proc Natl Acad Sci U S A 2008; 105:11146-51. [PMID: 18678891 DOI: 10.1073/pnas.0804506105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The widely used Born model describes the electrostatic response of continuous media using static dielectric constants. However, when applied to a liquid environment, a comparison of Born model predictions with experimental values (e.g., transfer free energies and pK(a) shifts) found that agreement is only achieved by using physically unrealistic dielectric constants for proteins, lipids, etc., and/or equally unrealistic atomic radii. This leads to questions concerning the physical origins for this failure of the Born model. We partially resolve this question by applying the Langevin-Debye (LD) model of a continuous distribution of point, polarizable dipoles, a model that contains an added dependence of the electrostatic response on the solvent's optical dielectric constant and both gas- and liquid-phase dipole moments, features absent in the Born model to which the LD model reduces for weak fields. The LD model is applied to simple representations of three biologically relevant systems: (i) globular proteins, (ii) lipid bilayers, and (iii) membrane proteins. The linear Born treatment greatly overestimates both the self-energy and the transfer free energy from water to hydrophobic environments (e.g., a protein interior). By using the experimental dielectric constant, the energy cost of charge burial in either globular or membrane proteins of the Born model is reduced by almost 50% with the nonlinear theory as is the pK(a) shift, and the shifts agree well with experimental trends.
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11
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Benbrahim N, Rahmouni A, Ruiz-López MF. A theoretical study of medium effects on the structure of the glycine analogue aminomethylphosphonic acid. Phys Chem Chem Phys 2008; 10:5624-32. [DOI: 10.1039/b804694h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Cordomí A, Edholm O, Perez JJ. Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. J Comput Chem 2007; 28:1017-30. [PMID: 17269123 DOI: 10.1002/jcc.20579] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The present study analyzes the effect of the simulation conditions on the results of molecular dynamics simulations of G-protein coupled receptors (GPCRs) performed with an explicit lipid bilayer. Accordingly, the present work reports the analysis of different simulations of bovine rhodopsin embedded in a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer using two different sampling conditions and two different approaches for the treatment of long-range electrostatic interactions. Specifically, sampling was carried out either by using the statistical ensembles NVT or NPT (constant number of atoms, a pressure of 1 atm in all directions and fixed temperature), and the electrostatic interactions were treated either by using a twin-cutoff, or the particle mesh Ewald summation method (PME). The results of the present study suggest that the use of the NPT ensemble in combination with the PME method provide more realistic simulations. The use of NPT during the equilibration avoids the need of an a priori estimation of the box dimensions, giving the correct area per lipid. However, once the system is equilibrated, the simulations are irrespective of the sampling conditions used. The use of an electrostatic cutoff induces artifacts on both lipid thickness and the ion distribution, but has no direct effect on the protein and water molecules.
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Affiliation(s)
- Arnau Cordomí
- Dept d'Enginyeria Química, Technical University of Catalonia (UPC), Av. Diagonal 647, 08028 Barcelona, Spain.
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13
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Richardson JC, Foster CS, Doughty SW, Burton JS, MacRae RJ, Melia CD. The influence of l-amino acid molecular structure on the phase transition temperature of hydroxypropyl methylcellulose. Carbohydr Polym 2006. [DOI: 10.1016/j.carbpol.2005.11.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Chan JC, Oyler NA, Yau WM, Tycko R. Parallel beta-sheets and polar zippers in amyloid fibrils formed by residues 10-39 of the yeast prion protein Ure2p. Biochemistry 2005; 44:10669-80. [PMID: 16060675 PMCID: PMC1380259 DOI: 10.1021/bi050724t] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the results of solid-state nuclear magnetic resonance (NMR) and atomic force microscopy measurements on amyloid fibrils formed by residues 10-39 of the yeast prion protein Ure2p (Ure2p(10)(-)(39)). Measurements of intermolecular (13)C-(13)C nuclear magnetic dipole-dipole couplings indicate that Ure2p(10)(-)(39) fibrils contain in-register parallel beta-sheets. Measurements of intermolecular (15)N-(13)C dipole-dipole couplings, using a new solid-state NMR technique called DSQ-REDOR, are consistent with hydrogen bonds between side chain amide groups of Gln18 residues. Such side chain hydrogen bonding interactions have been called "polar zippers" by M. F. Perutz and have been proposed to stabilize amyloid fibrils formed by peptides with glutamine- and asparagine-rich sequences, such as Ure2p(10)(-)(39). We propose that polar zipper interactions account for the in-register parallel beta-sheet structure in Ure2p(10)(-)(39) fibrils and that similar peptides will also exhibit parallel beta-sheet structures in amyloid fibrils. We present molecular models for Ure2p(10)(-)(39) fibrils that are consistent with available experimental data. Finally, we show that solid-state (13)C NMR chemical shifts for (13)C-labeled Ure2p(10)(-)(39) fibrils are insensitive to hydration level, indicating that the fibril structure is not affected by the presence or absence of bulk water.
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Key Words
- nmr, nuclear magnetic resonance
- aβ, β-amyloid peptide
- ure2p10–39, residues 10-39 of the ure2p yeast prion protein
- em, electron microscopy
- fmoc, 9-fluorenylmethoxycarbonyl
- tfa, trifluoroacetic acid
- afm, atomic force microscopy
- mas, magic-angle spinning
- fprfdr-ct, constant-time finite-pulse radiofrequency-driven recoupling
- redor, rotational echo double resonance
- dsq, double single-quantum
- tppm, two-pulse phase modulation
- csa, chemical shift anisotropy
- md, molecular dynamics
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Affiliation(s)
| | - Nathan A. Oyler
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
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15
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Affiliation(s)
- Jacopo Tomasi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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16
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Potter JA, Fyfe PK, Frolov D, Wakeham MC, van Grondelle R, Robert B, Jones MR. Strong Effects of an Individual Water Molecule on the Rate of Light-driven Charge Separation in the Rhodobacter sphaeroides Reaction Center. J Biol Chem 2005; 280:27155-64. [PMID: 15908429 DOI: 10.1074/jbc.m501961200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The role of a water molecule (water A) located between the primary electron donor (P) and first electron acceptor bacteriochlorophyll (B(A)) in the purple bacterial reaction center was investigated by mutation of glycine M203 to leucine (GM203L). The x-ray crystal structure of the GM203L reaction center shows that the new leucine residue packs in such a way that water A is sterically excluded from the complex, but the structure of the protein-cofactor system around the mutation site is largely undisturbed. The results of absorbance and resonance Raman spectroscopy were consistent with either the removal of a hydrogen bond interaction between water A and the keto carbonyl group of B(A) or a change in the local electrostatic environment of this carbonyl group. Similarities in the spectroscopic properties and x-ray crystal structures of reaction centers with leucine and aspartic acid mutations at the M203 position suggested that the effects of a glycine to aspartic acid substitution at the M203 position can also be explained by steric exclusion of water A. In the GM203L mutant, loss of water A was accompanied by an approximately 8-fold slowing of the rate of decay of the primary donor excited state, indicating that the presence of water A is important for optimization of the rate of primary electron transfer. Possible functions of this water molecule are discussed, including a switching role in which the redox potential of the B(A) acceptor is rapidly modulated in response to oxidation of the primary electron donor.
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Affiliation(s)
- Jane A Potter
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, United Kingdom
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17
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Gu W, Rahi SJ, Helms V. Solvation Free Energies and Transfer Free Energies for Amino Acids from Hydrophobic Solution to Water Solution from a Very Simple Residue Model. J Phys Chem B 2004. [DOI: 10.1021/jp0376424] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei Gu
- Center of Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany, and Max-Planck-Institute of Biophysics, D-60439 Frankfurt/M., Germany
| | - Sahand Jamal Rahi
- Center of Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany, and Max-Planck-Institute of Biophysics, D-60439 Frankfurt/M., Germany
| | - Volkhard Helms
- Center of Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany, and Max-Planck-Institute of Biophysics, D-60439 Frankfurt/M., Germany
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18
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Spiedel D, Jones MR, Robert B. Tuning of the redox potential of the primary electron donor in reaction centres of purple bacteria: effects of amino acid polarity and position. FEBS Lett 2002; 527:171-5. [PMID: 12220655 DOI: 10.1016/s0014-5793(02)03203-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mutation of residues His L168 and Phe M197 in the reaction centre from Rhodobacter sphaeroides has an unusually strong effect on the mid-point redox potential (E(m)) of the pair of bacteriochlorophylls that form the primary donor of electrons, tuning E(m) over a range of nearly 250 mV. This effect is correlated to the accompanying change in the permanent dipole of the L168 or M197 residue, suggesting it is mediated by changes in charge-dipole interactions. Comparisons with mutations made at a variety of other positions show that this correlation is particular to this residue pair, perhaps reflecting their proximity to the ring I regions of the dimer bacteriochlorophylls that form the overlap region between these molecules.
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Affiliation(s)
- Diane Spiedel
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, S10 2UH, Sheffield, UK
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19
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Sandberg L, Edholm O. Nonlinear response effects in continuum models of the hydration of ions. J Chem Phys 2002. [DOI: 10.1063/1.1435566] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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