The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures
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{"title"=>"The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures", "type"=>"journal", "authors"=>[{"first_name"=>"Erik", "last_name"=>"van Dijk", "scopus_author_id"=>"56022669100"}, {"first_name"=>"Arlo", "last_name"=>"Hoogeveen", "scopus_author_id"=>"56672575600"}, {"first_name"=>"Sanne", "last_name"=>"Abeln", "scopus_author_id"=>"8727728500"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "pui"=>"604784509", "pmid"=>"26000449", "isbn"=>"1553-7358", "doi"=>"10.1371/journal.pcbi.1004277", "sgr"=>"84930607387", "scopus"=>"2-s2.0-84930607387"}, "id"=>"e257d700-5244-38b7-bb57-cde878a38233", "abstract"=>"The hydrophobic effect is the main driving force in protein folding. One can estimate the relative strength of this hydrophobic effect for each amino acid by mining a large set of experimentally determined protein structures. However, the hydrophobic force is known to be strongly temperature dependent. This temperature dependence is thought to explain the denaturation of proteins at low temperatures. Here we investigate if it is possible to extract this temperature dependence directly from a large set of protein structures determined at different temperatures. Using NMR structures filtered for sequence identity, we were able to extract hydrophobicity propensities for all amino acids at five different temperature ranges (spanning 265-340 K). These propensities show that the hydrophobicity becomes weaker at lower temperatures, in line with current theory. Alternatively, one can conclude that the temperature dependence of the hydrophobic effect has a measurable influence on protein structures. Moreover, this work provides a method for probing the individual temperature dependence of the different amino acid types, which is difficult to obtain by direct experiment.", "link"=>"http://www.mendeley.com/research/hydrophobic-temperature-dependence-amino-acids-directly-calculated-protein-structures", "reader_count"=>45, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>15, "Neuroscience"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Business, Management and Accounting"=>1, "Physics and Astronomy"=>3, "Chemical Engineering"=>1, "Chemistry"=>6, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>6}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>5}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Japan"=>1, "United Kingdom"=>1, "India"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2079788"], "description"=>"<p>The cost of making a cavity in the water with a radius of the given size against temperature is plotted. The position of the maximum depends on the size (radius) of the solute. Small solutes with a radius of 4 Å have a peak at around 70°C, whereas larger particles with a radius of 10 Å have a peak around 40°C. <b>An example protein structure: PDB-ID: 2K5I (B).</b> We estimate free energies of transfer from the hydrophobic core to the surface of the protein by comparing the number of hydrophobic amino acids on the surface (small yellow spheres), to the number of buried hydrophobics (large yellow spheres), to the number of polar amino acids on the surface (small blue spheres) and to the number of buried polar amino acids (large blue spheres).</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423906, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.g001", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Length_scale_dependence_of_hydrophobic_effect_from_calculations_by_Huang_and_Chandler_10_A_/1423906", "title"=>"Length scale dependence of hydrophobic effect from calculations by Huang and Chandler [10] (A).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079789"], "description"=>"<p>All acquisition temperatures of structures as of April 2014 available in the PDB are shown. The 80,662 X-ray diffraction structures are centred around 100 K, while the 10,969 NMR structures show a peak at room temperature (300 K). Note that the small peak of NMR data just above absolute zero may be temperatures entered in celsius instead of kelvin; this data is not used in this study. Temperature bins, as given in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004277#pcbi.1004277.t001\" target=\"_blank\">Table 1</a>, are indicated in different shades of grey.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423907, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_temperatures_at_which_experimental_protein_structures_were_resolved_/1423907", "title"=>"Distribution of temperatures at which experimental protein structures were resolved.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079790"], "description"=>"<p>Contact based (A) and surface based (B) free energies are shown for different classes of amino acids. Points show the free energy estimates for each temperature bin, lines are fitted with a parabola, consistent with the potentials found in [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004277#pcbi.1004277.ref010\" target=\"_blank\">10</a>]. Arrows indicate the bins used to test the significance of the temperature dependence.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423908, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.g003", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Raw_free_energies_of_transfer_for_classes_of_amino_acids_/1423908", "title"=>"Raw free energies of transfer for classes of amino acids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079791"], "description"=>"<p>Contact based (A) and surface based (B) free energies are shown for hydrophobic and aromatic amino acids. The free energies are corrected by setting a reference of the polar and charged amino acids. Points show the free energy estimates for each temperature bin and lines are fitted with a parabola. Arrows indicate the bins used to test the significance of the temperature dependence.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423909, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.g004", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_corrected_free_energies_of_transfer_for_hydrophobic_amino_acids_/1423909", "title"=>"Reference corrected free energies of transfer for hydrophobic amino acids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079792"], "description"=>"<p>The number of NMR chains as present in the PDB before and after filtering is shown for different temperature bins (in kelvin). At the first stage of filtering, sequence bias was removed using PDB-select-25. At the last filtering step, chains were removed when they were not compatible with DSSP or when they had multiple and different acquisition temperatures.</p><p>Selected protein structures.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423910, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.t001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_protein_structures_/1423910", "title"=>"Selected protein structures.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079793"], "description"=>"<p>Amino acid class definition.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423911, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.t002", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acid_class_definition_/1423911", "title"=>"Amino acid class definition.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079794"], "description"=>"<p>The difference in free energy estimates (ΔΔ<i>G</i>) between the lowest temperature bin (265–290K) and room temperature (297–299K) is shown together with its significance (p-value) for each class of amino acids. The significance was tested using a resampling procedure. The amino acids are pooled according to defined classes; the free energy estimates are not reference corrected.</p><p>Significance of hydrophobic temperature dependence pooled.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423912, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.t003", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significance_of_hydrophobic_temperature_dependence_pooled_/1423912", "title"=>"Significance of hydrophobic temperature dependence pooled.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079795"], "description"=>"<p>The difference in free energy estimates (ΔΔ<i>G</i>) between the lowest temperature bin (265–290K) and room temperature (297–299K) is shown together with its significance (p-value) for each class of amino acids. The significance was tested using a resampling procedure. The hydrophobic and aromatic amino acids are shown and are reference corrected with respect to the charged and polar amino acids.</p><p>Significance of hydrophobic temperature dependence.</p>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423913, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004277.t004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significance_of_hydrophobic_temperature_dependence_/1423913", "title"=>"Significance of hydrophobic temperature dependence.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-22 03:19:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2079796", "https://ndownloader.figshare.com/files/2079797", "https://ndownloader.figshare.com/files/2079798", "https://ndownloader.figshare.com/files/2079799", "https://ndownloader.figshare.com/files/2079800", "https://ndownloader.figshare.com/files/2079801", "https://ndownloader.figshare.com/files/2079802", "https://ndownloader.figshare.com/files/2079803", "https://ndownloader.figshare.com/files/2079804", "https://ndownloader.figshare.com/files/2079805", "https://ndownloader.figshare.com/files/2079806", "https://ndownloader.figshare.com/files/2079807", "https://ndownloader.figshare.com/files/2079808", "https://ndownloader.figshare.com/files/2079809", "https://ndownloader.figshare.com/files/2079810", "https://ndownloader.figshare.com/files/2079811", "https://ndownloader.figshare.com/files/2079812", "https://ndownloader.figshare.com/files/2079813"], "description"=>"<div><p>The hydrophobic effect is the main driving force in protein folding. One can estimate the relative strength of this hydrophobic effect for each amino acid by mining a large set of experimentally determined protein structures. However, the hydrophobic force is known to be strongly temperature dependent. This temperature dependence is thought to explain the denaturation of proteins at low temperatures. Here we investigate if it is possible to extract this temperature dependence directly from a large set of protein structures determined at different temperatures. Using NMR structures filtered for sequence identity, we were able to extract hydrophobicity propensities for all amino acids at five different temperature ranges (spanning 265-340 K). These propensities show that the hydrophobicity becomes weaker at lower temperatures, in line with current theory. Alternatively, one can conclude that the temperature dependence of the hydrophobic effect has a measurable influence on protein structures. Moreover, this work provides a method for probing the individual temperature dependence of the different amino acid types, which is difficult to obtain by direct experiment.</p></div>", "links"=>[], "tags"=>["temperature dependence", "nmr", "Hydrophobic Temperature Dependence", "protein structures"], "article_id"=>1423914, "categories"=>["Biological Sciences"], "users"=>["Erik van Dijk", "Arlo Hoogeveen", "Sanne Abeln"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004277.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s002", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s003", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s004", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s005", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s006", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s007", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s008", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s009", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s010", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s011", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s012", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s013", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s014", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s015", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s016", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s017", "https://dx.doi.org/10.1371/journal.pcbi.1004277.s018"], "stats"=>{"downloads"=>27, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Hydrophobic_Temperature_Dependence_of_Amino_Acids_Directly_Calculated_from_Protein_Structures_/1423914", "title"=>"The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-05-22 03:19:27"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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