Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin
Publication Date
August 28, 2014
Journal
PLOS Computational Biology
Authors
Geir Villy Isaksen, Johan Åqvist & Bjørn Olav Brandsdal
Volume
10
Issue
8
Pages
e1003813
DOI
https://dx.plos.org/10.1371/journal.pcbi.1003813
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003813
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25165981
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148182
Europe PMC
http://europepmc.org/abstract/MED/25165981
Web of Science
000341573600049
Scopus
84923152178
Mendeley
http://www.mendeley.com/research/protein-surface-softness-origin-enzyme-coldadaptation-trypsin
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/1653170"], "description"=>"<p>Key mutations between bovine and salmon trypsin and their location in the 3D structure, identified based on sequence alignments (inset below) of several warm-active vs cold-active trypsins. A red sphere indicates that a neutral residue in bovine trypsin is mutated to a charged one in salmon trypsin, whereas a blue sphere denotes the reverse type of substitution, and a green sphere denotes a neutral residue in both trypsins. Abbreviations used: AST - anionic salmon trypsin, AFT - Antarctic fish trypsin, CT1 - Atlantic cod trypsin, CST - cationic salmon trypsin, RT - rat trypsin, PT - Pig trypsin and BT - bovine trypsin.</p>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154107, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003813.g003", "stats"=>{"downloads"=>2, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Important_mutations_between_bovine_and_salmon_trypsin_/1154107", "title"=>"Important mutations between bovine and salmon trypsin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-28 02:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1653178"], "description"=>"<p>(<b>a</b>) Average backbone RMSF profiles in the reactant state for native bovine trypsin and the N97Y mutant and (<b>b</b>) for native salmon trypsin and theY97N mutant.</p>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154115, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003813.g005", "stats"=>{"downloads"=>3, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_residual_fluctuations_for_native_and_mutant_trypsins_/1154115", "title"=>"Comparison of residual fluctuations for native and mutant trypsins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-28 02:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1653160"], "description"=>"<p>(a) Calculated free energy profiles (300 K) for tetrahedral intermediate formation in the acylation step of bovine trypsin (BT), anionic salmon trypsin (AST) and in the imidazole catalyzed reference reaction in water. (b) The clear difference in slopes from the calculated Arrhenius plots (ΔG<sup>‡</sup>/T vs 1/T) for BT (red) and AST (blue) demonstrate that cold adapted trypsin has a lower activation enthalpy compared to the warm-active ortholog.</p>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154097, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003813.g001", "stats"=>{"downloads"=>2, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_free_energy_profiles_and_Arrhenius_plots_/1154097", "title"=>"Comparison of free energy profiles and Arrhenius plots.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-28 02:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1653177"], "description"=>"<p>(a) Disruption of an H-bond network by mutation of polar residue into a less polar (Asn97Tyr). (b) Disruption of an H-bond network by mutation of a polar residue into a charged one (Ser110Lys). (c) Complete change of H-bond network and loop orientation (Ser150Asp and correlated muations). (d) Destabilization of the packing of hydrophobic surface patches by mutation of a nonpolar residue into a charged one (Val 90Arg).</p>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154114, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003813.g004", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanisms_for_increasing_surface_softness_in_salmon_trypsin_cyan_relative_to_bovine_red_trypsin_/1154114", "title"=>"Mechanisms for increasing surface softness in salmon trypsin (cyan) relative to bovine (red) trypsin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-28 02:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1653180", "https://ndownloader.figshare.com/files/1653181", "https://ndownloader.figshare.com/files/1653182", "https://ndownloader.figshare.com/files/1653183"], "description"=>"<div><p>Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions. Cold-loving organisms (psychrophiles) express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures. A remarkable universal characteristic of cold-active enzymes is that they show a reduction both in activation enthalpy and entropy, compared to mesophilic orthologs, which makes their reaction rates less sensitive to falling temperature. Despite significant efforts since the early 1970s, the important question of the origin of this effect still largely remains unanswered. Here we use cold- and warm-active trypsins as model systems to investigate the temperature dependence of the reaction rates with extensive molecular dynamics free energy simulations. The calculations quantitatively reproduce the catalytic rates of the two enzymes and further yield high-precision Arrhenius plots, which show the characteristic trends in activation enthalpy and entropy. Detailed structural analysis indicates that the relationship between these parameters and the 3D structure is reflected by significantly different internal protein energy changes during the reaction. The origin of this effect is not localized to the active site, but is found in the outer regions of the protein, where the cold-active enzyme has a higher degree of softness. Several structural mechanisms for softening the protein surface are identified, together with key mutations responsible for this effect. Our simulations further show that single point-mutations can significantly affect the thermodynamic activation parameters, indicating how these can be optimized by evolution.</p></div>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154117, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003813.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003813.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003813.s003", "https://dx.doi.org/10.1371/journal.pcbi.1003813.s004"], "stats"=>{"downloads"=>12, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_Surface_Softness_Is_the_Origin_of_Enzyme_Cold_Adaptation_of_Trypsin_/1154117", "title"=>"Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-28 02:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1653165"], "description"=>"<p>(a) Average protein backbone fluctuations for bovine (BT) and salmon (AST) trypsin during 100 ns of MD in the reactant state. (b) The percentage of residues with RMSFs>1.1 Å, in spherical regions centered on the active site, indicate that both enzymes have a hard core and a softer outer region, in which AST has a higher prevalence of mobile residues.</p>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154102, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003813.g002", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Residual_fluctuations_and_structural_location_of_mobile_residues_/1154102", "title"=>"Residual fluctuations and structural location of mobile residues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-28 02:48:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1653179"], "description"=>"<p>*Subscripts rr, rs and ss denote, respectively, interactions among atoms in the EVB region, their interactions with the surroundings, and the internal interactions within the surroundings.</p><p>Error bars denote standard error of the mean.</p><p>Calculated thermodynamic activation parameters (kcal/mol) for native and mutant bovine (BT) and salmon (AST) trypsins at 300 K.</p>", "links"=>[], "tags"=>["entropy", "reaction rates", "enzyme", "protein energy changes", "simulation", "origin", "Protein Surface Softness", "parameter", "activation enthalpy", "3 D structure", "organism"], "article_id"=>1154116, "categories"=>["Biological Sciences"], "users"=>["Geir Villy Isaksen", "Johan Åqvist", "Bjørn Olav Brandsdal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003813.t001", "stats"=>{"downloads"=>6, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Calculated_thermodynamic_activation_parameters_kcal_mol_for_native_and_mutant_bovine_BT_and_salmon_AST_trypsins_at_300_K_/1154116", "title"=>"Calculated thermodynamic activation parameters (kcal/mol) for native and mutant bovine (BT) and salmon (AST) trypsins at 300 K.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-28 02:48:01"}

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Relative Metric

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