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Diaz A, Ramakrishnan V. Effect of osmolytes on the EcoRI endonuclease: Insights into hydration and protein dynamics from molecular dynamics simulations. Comput Biol Chem 2023; 105:107883. [PMID: 37210944 DOI: 10.1016/j.compbiolchem.2023.107883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Osmolytes play an important role in cellular physiology by modulating the properties of proteins, including their molecular specificity. EcoRI is a model restriction enzyme whose specificity to DNA is altered in the presence of osmolytes. Here, we investigate the effect of two different osmolytes, glycerol and DMSO, on the dynamics and hydration of the EcoRI enzyme using molecular dynamics simulations. Our results show that the osmolytes, alter the essential dynamics of EcoRI. Particularly, we observe that the dynamics of the arm region of EcoRI which is involved in DNA binding is significantly altered. In addition, conformational free energy analyses reveals that the osmolytes bring about a change in the landscape similar to that of EcoRI bound to cognate DNA. We further observe that the hydration of the enzyme for each of the osmolyte is different, indicating that the mechanism of action of each of these osmolytes could be different. Further analyses of interfacial water dynamics using rotational autocorrelation function reveals that while the protein surface contributes to a slower tumbling motion of water, osmolytes, additionally contribute to the slowing of the angular motion of the water molecules. Entropy analysis also corroborates with this finding. We also find that the slowed rotational motion of interfacial waters in the presence of osmolytes contributes to a slowed relaxation of the hydrogen bonds between the interfacial waters and the functionally important residues in the protein. Taken together, our results show that osmolytes alter the dynamics of the protein by altering the dynamics of water. This altered dynamics, mediated by the changes in the water dynamics and hydrogen bonds with functionally important residues, may contribute to the altered specificity of EcoRI in the presence of osmolytes.
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Affiliation(s)
- Aathithya Diaz
- Computational Molecular Biophysics Laboratory, Bioinformatics Center, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamil Nadu, India
| | - Vigneshwar Ramakrishnan
- Computational Molecular Biophysics Laboratory, Bioinformatics Center, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamil Nadu, India.
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2
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Diaz A, Jothiraman HB, Ramakrishnan V. Effect of glycerol on free DNA: A molecular dynamics simulation study. J Mol Graph Model 2022; 114:108169. [DOI: 10.1016/j.jmgm.2022.108169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
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3
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Mandal SC, Maganti L, Mondal M, Chakrabarti J. Microscopic insight to specificity of metal ion cofactor in DNA cleavage by restriction endonuclease EcoRV. Biopolymers 2020; 111:e23396. [PMID: 32858776 DOI: 10.1002/bip.23396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 11/06/2022]
Abstract
Restriction endonucleases protect bacterial cells against bacteriophage infection by cleaving the incoming foreign DNA into fragments. In presence of Mg2+ ions, EcoRV is able to cleave the DNA but not in presence of Ca2+ , although the protein binds to DNA in presence of both metal ions. We make an attempt to understand this difference using conformational thermodynamics. We calculate the changes in conformational free energy and entropy of conformational degrees of freedom, like DNA base pair steps and dihedral angles of protein residues in Mg2+ (A)-EcoRV-DNA complex compared to Ca2+ (S)-EcoRV-DNA complex using all-atom molecular dynamics (MD) trajectories of the complexes. We find that despite conformational stability and order in both complexes, the individual degrees of freedom behave differently in the presence of two different metal ions. The base pairs in cleavage region are highly disordered in Ca2+ (S)-EcoRV-DNA compared to Mg2+ (A)-EcoRV-DNA. One of the acidic residues ASP90, coordinating to the metal ion in the vicinity of the cleavage site, is conformationally destabilized and disordered, while basic residue LYS92 gets conformational stability and order in Ca2+ (S) bound complex than in Mg2+ (A) bound complex. The enhanced fluctuations hinder placement of the metal ion in the vicinity of the scissile phosphate of DNA. Similar loss of conformational stability and order in the cleavage region is observed by the replacement of the metal ion. Considering the placement of the metal ion near scissile phosphate as requirement for cleavage action, our results suggest that the changes in conformational stability and order of the base pair steps and the protein residues lead to cofactor sensitivity of the enzyme. Our method based on fluctuations of microscopic conformational variables can be applied to understand enzyme activities in other protein-DNA systems.
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Affiliation(s)
- Sasthi Charan Mandal
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Manas Mondal
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen, China
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, India.,Thematic Unit of Excellence on Computational Materials Science, and Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
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4
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Abstract
Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species loaded into the same well. However, shift assays can access only a subset of reaction possibilities that could be otherwise seen if separate bands of reagent species might instead be collisionally reacted. Here, we adapt gel electrophoresis by fabricating two or more wells in the same lane, loading these wells with different reagent species, and applying an electric field, thereby producing collisional reactions between propagating pulse-like bands of these species, which we image optically. For certain pairs of anionic and cationic dyes, propagating bands pass through each other unperturbed; yet, for other pairs, we observe complexing and precipitation reactions, indicating strong attractive interactions. We generalize this band-collision gel electrophoresis (BCGE) approach to other reaction types, including acid-base, ligand exchange, and redox, as well as to colloidal species in passivated large-pore gels. Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species, but these assays access only a subset of reaction possibilities. Here, the authors develop a band-collision gel electrophoresis (BCGE) approach that demonstrates a much wider variety of reaction types.
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5
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Albrecht AV, Kim HM, Poon GMK. Mapping interfacial hydration in ETS-family transcription factor complexes with DNA: a chimeric approach. Nucleic Acids Res 2019; 46:10577-10588. [PMID: 30295801 PMCID: PMC6237740 DOI: 10.1093/nar/gky894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/21/2018] [Indexed: 11/12/2022] Open
Abstract
Hydration of interfaces is a major determinant of target specificity in protein/DNA interactions. Interfacial hydration is a highly variable feature in DNA recognition by ETS transcription factors and functionally relates to cellular responses to osmotic stress. To understand how hydration is mediated in the conserved ETS/DNA binding interface, secondary structures comprising the DNA contact surface of the strongly hydrated ETS member PU.1 were substituted, one at a time, with corresponding elements from its sparsely hydrated relative Ets-1. The resultant PU.1/Ets-1 chimeras exhibited variably reduced sensitivity to osmotic pressure, indicative of a distributed pattern of interfacial hydration in wildt-ype PU.1. With the exception of the recognition helix H3, the chimeras retained substantially high affinities. Ets-1 residues could therefore offset the loss of favorable hydration contributions in PU.1 via low-water interactions, but at the cost of decreased selectivity at base positions flanking the 5'-GGA-3' core consensus. Substitutions within H3 alone, which contacts the core consensus, impaired binding affinity and PU.1 transactivation in accordance with the evolutionary separation of the chimeric residues involved. The combined biophysical, bioinformatics and functional data therefore supports hydration as an evolved specificity determinant that endows PU.1 with more stringent sequence selection over its ancestral relative Ets-1.
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Affiliation(s)
- Amanda V Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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6
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Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L. Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex. Biochemistry 2016; 55:6115-6132. [PMID: 27786446 PMCID: PMC5402698 DOI: 10.1021/acs.biochem.6b00919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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Metal
ion cofactors can alter the energetics and specificity of
sequence specific protein–DNA interactions, but it is unknown
if the underlying effects on structure and dynamics are local or dispersed
throughout the protein–DNA complex. This work uses EcoRV endonuclease
as a model, and catalytically inactive lanthanide ions, which replace
the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations
indicate that four Lu3+ or two La3+ cations
bind, and two new crystal structures confirm that Lu3+ binding
is confined to the active sites. NMR spectra show that the metal-free
EcoRV complex with cognate (GATATC) DNA is structurally distinct from
the nonspecific complex, and that metal ion binding sites are not
assembled in the nonspecific complex. NMR chemical shift perturbations
were determined for 1H–15N amide resonances,
for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical
shifts throughout the cognate complex are unperturbed, so metal binding
does not induce major conformational changes. However, some large
perturbations of amide and side chain methyl resonances occur as far
as 34 Å from the metal ions. Concerted changes in specific residues
imply that local effects of metal binding are propagated via a β-sheet
and an α-helix. Both amide and methyl resonance perturbations
indicate changes in the interface between subunits of the EcoRV homodimer.
Bound metal ions also affect amide hydrogen exchange rates for distant
residues, including a distant subdomain that contacts DNA phosphates
and promotes DNA bending, showing that metal ions in the active sites,
which relieve electrostatic repulsion between protein and DNA, cause
changes in slow dynamics throughout the complex.
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Affiliation(s)
- Kaustubh Sinha
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.,Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Sahil S Sangani
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Andrew D Kehr
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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7
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Kurian P, Dunston G, Lindesay J. How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases. J Theor Biol 2016; 391:102-12. [PMID: 26682627 PMCID: PMC4746125 DOI: 10.1016/j.jtbi.2015.11.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 10/29/2015] [Accepted: 11/15/2015] [Indexed: 10/22/2022]
Abstract
Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism.
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Affiliation(s)
- P Kurian
- National Human Genome Center, Howard University College of Medicine, Washington, DC 20059, USA; Department of Physics and Astronomy, Howard University, Washington, DC 20059, USA; Computational Physics Laboratory, Howard University, Washington, DC 20059, USA.
| | - G Dunston
- National Human Genome Center, Howard University College of Medicine, Washington, DC 20059, USA; Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA
| | - J Lindesay
- Department of Physics and Astronomy, Howard University, Washington, DC 20059, USA; Computational Physics Laboratory, Howard University, Washington, DC 20059, USA
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8
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Rye-McCurdy T, Rouzina I, Musier-Forsyth K. Fluorescence anisotropy-based salt-titration approach to characterize protein-nucleic acid interactions. Methods Mol Biol 2015; 1259:385-402. [PMID: 25579598 DOI: 10.1007/978-1-4939-2214-7_23] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Many proteins bind nucleic acids (NA) via cationic residues that interact electrostatically with the anionic phosphate backbone of RNA or DNA. These electrostatic interactions are often insensitive to NA sequence and structure, but confer strong salt dependence to the binding interactions. In contrast, salt-independent non-electrostatic contacts reflect more specific binding interactions. Proteins with multiple cationic NA-binding domains connected by flexible linkers, such as the HIV-1 Gag polyprotein, may bind different NA molecules in distinct ways. For example, Gag binding to the Psi-packaging signal of the HIV-1 RNA genome optimizes the specific non-electrostatic binding component of this protein-RNA interaction. In contrast, Gag binding to a non-psi RNA optimizes the electrostatic interactions at the expense of specific contacts. Here, we describe a fluorescence anisotropy-based salt-titration approach that allows complete characterization of both electrostatic and non-electrostatic binding components for any protein-NA complex in a quantitative manner within a single assay.
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Affiliation(s)
- Tiffiny Rye-McCurdy
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, Centers for Retroviral Research and RNA Biology, The Ohio State University, 100 West 18th Ave., Columbus, OH, 43210-1340, USA
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9
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Pollak AJ, Chin AT, Reich NO. Distinct facilitated diffusion mechanisms by E. coli Type II restriction endonucleases. Biochemistry 2014; 53:7028-37. [PMID: 25350874 DOI: 10.1021/bi501110r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The passive search by proteins for particular DNA sequences involving nonspecific DNA is essential for gene regulation, DNA repair, phage defense, and diverse epigenetic processes. Distinct mechanisms contribute to these searches, and it remains unresolved as to which mechanism or blend of mechanisms best suits a particular protein and, more importantly, its biological role. To address this, we compare the translocation properties of two well-studied bacterial restriction endonucleases (ENases), EcoRI and EcoRV. These dimeric, magnesium-dependent enzymes hydrolyze related sites (EcoRI ENase, 5'-GAATTC-3'; EcoRV ENase, 5'-GATATC-3'), leaving overhangs and blunt DNA segments, respectively. Here, we demonstrate that the extensive sliding by EcoRI ENase, involving sliding up to ∼600 bp prior to dissociating from the DNA, contrasts with a larger reliance on hopping mechanism(s) by EcoRV ENase. The mechanism displayed by EcoRI ENase results in a highly thorough search of DNA, whereas the EcoRV ENase mechanism results in an extended, yet less rigorous, interrogation of DNA sequence space. We describe how these mechanistic distinctions are complemented by other aspects of these endonucleases, such as the 10-fold higher in vivo concentrations of EcoRI ENase compared to that of EcoRV ENase. Further, we hypothesize that the highly diverse enzyme arsenal that bacteria employ against foreign DNA involves seemingly similar enzymes that rely on distinct but complementary search mechanisms. Our comparative approach reveals how different proteins utilize distinct site-locating strategies.
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Affiliation(s)
- Adam J Pollak
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
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10
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Ferrandino R, Sidorova N, Rau D. Using single-turnover kinetics with osmotic stress to characterize the EcoRV cleavage reaction. Biochemistry 2014; 53:235-46. [PMID: 24328115 DOI: 10.1021/bi401089y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II restriction endonucleases require metal ions to specifically cleave DNA at canonical sites. Despite the wealth of structural and biochemical information, the number of Mg(2+) ions used for cleavage by EcoRV, in particular, at physiological divalent ion concentrations has not been established. In this work, we employ a single-turnover technique that uses osmotic stress to probe reaction kinetics between an initial specific EcoRV-DNA complex formed in the absence of Mg(2+) and the final cleavage step. With osmotic stress, complex dissociation before cleavage is minimized and the reaction rates are slowed to a convenient time scale of minutes to hours. We find that cleavage occurs by a two-step mechanism that can be characterized by two rate constants. The dependence of these rate constants on Mg(2+) concentration and osmotic pressure gives the number of Mg(2+) ions and water molecules coupled to each kinetic step of the EcoRV cleavage reaction. Each kinetic step is coupled to the binding 1.5-2.5 Mg(2+) ions, the uptake of ∼30 water molecules, and the cleavage of a DNA single strand. We suggest that each kinetic step reflects an independent, rate-limiting conformational change of each monomer of the dimeric enzyme that allows Mg(2+) ion binding. This modified single-turnover protocol has general applicability for metalloenzymes.
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Affiliation(s)
- Rocco Ferrandino
- The Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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11
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Vagenende V, Han AX, Pek HB, Loo BLW. Quantifying the molecular origins of opposite solvent effects on protein-protein interactions. PLoS Comput Biol 2013; 9:e1003072. [PMID: 23696727 PMCID: PMC3656110 DOI: 10.1371/journal.pcbi.1003072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/11/2013] [Indexed: 12/21/2022] Open
Abstract
Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology Institute, ASTAR (Agency for Science, Technology and Research), Singapore.
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12
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Sidorova NY, Scott T, Rau DC. DNA concentration-dependent dissociation of EcoRI: direct transfer or reaction during hopping. Biophys J 2013; 104:1296-303. [PMID: 23528089 DOI: 10.1016/j.bpj.2013.01.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/16/2013] [Accepted: 01/18/2013] [Indexed: 11/29/2022] Open
Abstract
Direct transfer of proteins between DNA helices is a recognized important feature of the recognition site search process. Direct transfer is characterized by a dissociation rate that depends on total DNA concentration. This is taken as evidence for the formation of an intermediate DNA-protein-DNA ternary complex. We find that the dissociation rate of EcoRI-DNA-specific complexes at 80 mM NaCl depends on the concentration of competitor oligonucleotide suggesting that direct transfer contributes to EcoRI dissociation. This dependence on competitor DNA concentration is not seen at 180 mM salt. A careful examination of the salt concentration dependence of the dissociation rate, however, shows that the predictions for the formation of a ternary complex are not observed experimentally. The findings can be rationalized by considering that just after dissociating from a DNA fragment the protein remains in close proximity to that fragment, can reassociate with it, and diffuse back to the recognition site rather than bind to an oligonucleotide in solution, a hopping excursion. The probability that a protein will bind to an oligonucleotide during a hop can be approximately calculated and shown to explain the data. A dependence of the dissociation rate of a DNA-protein complex on competitor DNA concentration does not necessarily mean direct transfer.
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Affiliation(s)
- Nina Y Sidorova
- The Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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13
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Zahran M, Berezniak T, Imhof P, Smith JC. Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease. FEBS Lett 2011; 585:2739-43. [DOI: 10.1016/j.febslet.2011.07.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/20/2011] [Accepted: 07/25/2011] [Indexed: 10/17/2022]
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