Ca2+ Binding Enhanced Mechanical Stability of an Archaeal Crystallin
Publication Date
April 11, 2014
Journal
PLOS ONE
Authors
Venkatraman Ramanujam, Hema Chandra Kotamarthi & Sri Rama Koti Ainavarapu
Volume
9
Issue
4
Pages
e94513
DOI
https://dx.plos.org/10.1371/journal.pone.0094513
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0094513
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24728085
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984160
Europe PMC
http://europepmc.org/abstract/MED/24728085
Web of Science
000336736200087
Scopus
84899636482
Mendeley
http://www.mendeley.com/research/ca2-binding-enhanced-mechanical-stability-archaeal-crystallin
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1461174"], "description"=>"<div><p>Structural topology plays an important role in protein mechanical stability. Proteins with β-sandwich topology consisting of Greek key structural motifs, for example, I27 of muscle titin and <sup>10</sup>FNIII of fibronectin, are mechanically resistant as shown by single-molecule force spectroscopy (SMFS). In proteins with β-sandwich topology, if the terminal strands are directly connected by backbone H-bonding then this geometry can serve as a “mechanical clamp”. Proteins with this geometry are shown to have very high unfolding forces. Here, we set out to explore the mechanical properties of a protein, M-crystallin, which belongs to β-sandwich topology consisting of Greek key motifs but its overall structure lacks the “mechanical clamp” geometry at the termini. M-crystallin is a Ca<sup>2+</sup> binding protein from <i>Methanosarcina acetivorans</i> that is evolutionarily related to the vertebrate eye lens β and γ-crystallins. We constructed an octamer of crystallin, (M-crystallin)<sub>8</sub>, and using SMFS, we show that M-crystallin unfolds in a two-state manner with an unfolding force ∼90 pN (at a pulling speed of 1000 nm/sec), which is much lower than that of I27. Our study highlights that the β-sandwich topology proteins with a different strand-connectivity than that of I27 and <sup>10</sup>FNIII, as well as lacking “mechanical clamp” geometry, can be mechanically resistant. Furthermore, Ca<sup>2+</sup> binding not only stabilizes M-crystallin by 11.4 kcal/mol but also increases its unfolding force by ∼35 pN at the same pulling speed. The differences in the mechanical properties of apo and holo M-crystallins are further characterized using pulling speed dependent measurements and they show that Ca<sup>2+</sup> binding reduces the unfolding potential width from 0.55 nm to 0.38 nm. These results are explained using a simple two-state unfolding energy landscape.</p></div>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "binding", "enhanced", "archaeal", "crystallin"], "article_id"=>996347, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513", "stats"=>{"downloads"=>15, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Ca_2_Binding_Enhanced_Mechanical_Stability_of_an_Archaeal_Crystallin/996347", "title"=>"Ca<sup>2+</sup> Binding Enhanced Mechanical Stability of an Archaeal Crystallin", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461168"], "description"=>"<p>The unfolding force histograms at various Ca<sup>2+</sup> concentrations are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094513#pone.0094513.s001\" target=\"_blank\">Figure S7 in File S1</a>. The increase in unfolding force in two phases is consistent with two Ca<sup>2+</sup> binding sites (see text for more details).</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "unfolding", "forces"], "article_id"=>996341, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.g004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ca_2_dependent_unfolding_forces_of_M_crystallin_8_/996341", "title"=>"[Ca<sup>2+</sup>] dependent unfolding forces of (M-crystallin)<sub>8</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461167"], "description"=>"<p>(<i>A</i>) A pair of FX traces obtained in the presence of 10 mM Ca<sup>2+</sup>. The contour length change upon unfolding is ∼29 nm and the unfolding force is ∼125 pN in the sawtooth curves (black). WLC fits are also shown (grey). (<i>B</i>) The unfolding force histograms of (M-crystallin)<sub>8</sub> in holo (filled) and apo (unfilled) show that Ca<sup>2+</sup> stabilizes the protein mechanically by ∼35 pN.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "unfolding", "bound"], "article_id"=>996340, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanical_unfolding_of_Ca_2_bound_M_crystallin_8_/996340", "title"=>"Mechanical unfolding of Ca<sup>2+</sup> bound (M-crystallin)<sub>8</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461172"], "description"=>"†<p>The ‘n’ in the parentheses is the number of events used in the analysis.</p><p>*mean ± SD.</p>‡<p>Monte Carlo simulation.</p>§<p>Bell-Evans-Ritchie approximation.</p>a<p>the range is obtained by using the average unfolding force ± SD in Monte Carlo simulations (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094513#pone.0094513.s001\" target=\"_blank\">Supporting Material in File S1</a>).</p>b<p>the errors obtained from the range of k<sub>u</sub><sup>o</sup>.</p>¶<p>k<sub>s</sub> calculated from Monte Carlo values of k<sub>u</sub><sup>0</sup> and Δx<sub>u.</sub></p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics"], "article_id"=>996345, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanical_properties_of_M_crystallin_/996345", "title"=>"Mechanical properties of M-crystallin.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461170"], "description"=>"<p>Ligand binding not only stabilizes the native state (N) by ΔG∼11.4 kcal/mol but also reduces the unfolding potential width (Δx<sub>u</sub>) from 0.55 nm to 0.38 nm. Estimates of unfolding transition state (TS) energy barriers (ΔG<sup>‡</sup>) are also indicated. See text and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094513#pone-0094513-t001\" target=\"_blank\">Tables 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094513#pone-0094513-t002\" target=\"_blank\">2</a> for more details.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "schematic", "two-state", "diagram", "depicting", "thermodynamic", "stabilization", "m-crystallin"], "article_id"=>996343, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.g006", "stats"=>{"downloads"=>0, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_schematic_of_two_state_energy_level_diagram_depicting_the_thermodynamic_and_mechanical_stabilization_of_M_crystallin_upon_Ca_2_binding_/996343", "title"=>"A schematic of two-state energy level diagram depicting the thermodynamic and mechanical stabilization of M-crystallin upon Ca<sup>2+</sup> binding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461171"], "description"=>"<p>Thermodynamic parameters of two Ca<sup>2+</sup> binding sites in M-crystallin monomer and octamer.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "binding", "sites", "m-crystallin", "monomer"], "article_id"=>996344, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.t001", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Thermodynamic_parameters_of_two_Ca_2_binding_sites_in_M_crystallin_monomer_and_octamer_/996344", "title"=>"Thermodynamic parameters of two Ca<sup>2+</sup> binding sites in M-crystallin monomer and octamer.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461169"], "description"=>"<p>A semi-logarithmic plot of unfolding force versus pulling speed for apo protein (○) and holo protein (•). Errors bars in the experimental data are SE. The Monte Carlo fits (solid line) are also shown for apo and holo proteins. Results from Monte Carlo simulations are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094513#pone-0094513-t002\" target=\"_blank\">Table 2</a>. It is evident from the data that Ca<sup>2+</sup> binding mechanically stabilizes M-crystallin by ∼30 pN at all pulling speeds.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "dependence", "unfolding"], "article_id"=>996342, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pulling_speed_dependence_on_mechanical_unfolding_of_M_crystallin_8_/996342", "title"=>"Pulling speed dependence on mechanical unfolding of (M-crystallin)<sub>8</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461166"], "description"=>"<p>(<i>A</i>) A pair of typical single-molecule force extension (FX) traces of apo protein (black). A series of equidistant force peaks in FX traces indicating the sequential unfolding of individual M-crystallin units in the octamer during the mechanical stretching (pulling speed is 1000 nm/s). The unfolding force peaks in sawtooth pattern are fitted with WLC model (grey). The contour length change is ∼29 nm and the unfolding force is ∼90 pN. Histograms of contour length change fitted to Gaussian distribution (<i>B</i>) and unfolding force (<i>C</i>) are shown.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "unfolding"], "article_id"=>996339, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanical_unfolding_of_M_crystallin_8_using_SMFS_/996339", "title"=>"Mechanical unfolding of (M-crystallin)<sub>8</sub> using SMFS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-11 03:00:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1461165"], "description"=>"<p>The pulling direction used in the single-molecule force spectroscopy (SMFS) experiments is shown by arrows. (<i>A</i>) NMR structure of I27 (PDB ID: 1TIT). Terminal β-strands A′ and G are directly connected by H-bonding, shearing this “mechanical-clamp” results in the mechanical unfolding of the protein. The rupture of H-bonds between A and B strands constitutes the less stable mechanical intermediate. (<i>B</i>) 2D topology diagram of I27. The five-stranded (BCDEF) ‘double’ Greek key (3,2)<sub>3</sub> formed by overlapping (3,1)<sub>N</sub> and (2,2)<sub>C</sub> Greek keys (as defined by Hutchinson and Thornton <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094513#pone.0094513-Hutchinson1\" target=\"_blank\">[53]</a>). (<i>C</i>) NMR structure of M-crystallin (PDB ID: 2K1W) bound to two Ca<sup>2+</sup> ions (shown as black spheres). The terminal β-strands A and H are not directly bonded and they need to be “peeled” away from each other to unfold the protein. (<i>D</i>) 2D topology diagram of M-crystallin showing the two (3,1)<sub>C</sub> Greek keys formed by ABCD and EFGH. In both cases, the backbone H-bonding around the terminal strands is shown.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Protein folding", "Protein interactions", "Structural proteins", "proteomics", "Spectrometric identification of proteins", "Biomacromolecule-ligand interactions", "Protein chemistry", "biophysics", "2d", "topology", "diagram", "greek", "motifs"], "article_id"=>996338, "categories"=>["Biological Sciences"], "users"=>["Venkatraman Ramanujam", "Hema Chandra Kotamarthi", "Sri Rama Koti Ainavarapu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094513.g001", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_and_2D_topology_diagram_of_two_946_sandwich_proteins_with_Greek_key_motifs_used_in_this_study_/996338", "title"=>"Structure and 2D topology diagram of two β-sandwich proteins with Greek key motifs used in this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-11 03:00:37"}

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Relative Metric

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