Protein Molecular Surface Mapped at Different Geometrical Resolutions
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{"title"=>"Protein Molecular Surface Mapped at Different Geometrical Resolutions", "type"=>"journal", "authors"=>[{"first_name"=>"Dan V.", "last_name"=>"Nicolau", "scopus_author_id"=>"7101984792"}, {"first_name"=>"Ewa", "last_name"=>"Paszek", "scopus_author_id"=>"24171709600"}, {"first_name"=>"Florin", "last_name"=>"Fulga", "scopus_author_id"=>"6603419884"}, {"first_name"=>"Dan V.", "last_name"=>"Nicolau", "scopus_author_id"=>"56861225000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23516572", "doi"=>"10.1371/journal.pone.0058896", "issn"=>"19326203", "pui"=>"368535205", "sgr"=>"84875014036", "scopus"=>"2-s2.0-84875014036"}, "id"=>"d5371b72-6c2e-36f4-94f7-bbbd7a58ad5b", "abstract"=>"Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.", "link"=>"http://www.mendeley.com/research/protein-molecular-surface-mapped-different-geometrical-resolutions", "reader_count"=>10, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>8, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Germany"=>2, "Russia"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/988414"], "description"=>"<p>Left: hydrophobic area (a1, top); ratio of hydrophobic per total area (a2, middle); and relative decrease of the hydrophobic area, reported to its maximum extent at minimum probe radius, (a3, bottom) for five model proteins: 1LZY  =  lysozyme; 1AFU  =  ribonuclease-A; 1Y4F  =  human hemoglobin; 1AO6  =  human serum albumin; and 1HZH  =  intact human IgG. Right: negatively charged area (b1, top); ratio of negatively charged per total area (b2, middle); and relative decrease of the negatively charged area, reported to its maximum extent at minimum probe radius (b3, bottom) for the same model proteins.</p>", "links"=>[], "tags"=>["negatively", "charged-related", "areas", "modulated", "probe"], "article_id"=>652909, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g005", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrophobicity_related_areas_and_negatively_charged_related_areas_modulated_by_the_probe_radius_/652909", "title"=>"Hydrophobicity-related areas; and negatively charged-related areas modulated by the probe radius.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:20:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/988413"], "description"=>"<p>The probing is performed with increasingly large probe radius (from left to right), as charges (top row, red  =  negative, blue  =  positive), and amphiphilicity (bottom row; blue  =  hydrophilic; red  =  hydrophilic).</p>", "links"=>[], "tags"=>["ribonuclease", "represented", "molecular"], "article_id"=>652908, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Physico_chemical_properties_of_ribonuclease_represented_on_its_molecular_surface_/652908", "title"=>"Physico-chemical properties of ribonuclease represented on its molecular surface.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:20:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007301"], "description"=>"<p>Definition of the properties measured on the protein molecular surface.</p>", "links"=>[], "tags"=>["molecular"], "article_id"=>667925, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.t002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Definition_of_the_properties_measured_on_the_protein_molecular_surface_/667925", "title"=>"Definition of the properties measured on the protein molecular surface.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-14 02:12:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/988403"], "description"=>"<p>The amphiphilic (blue – hydrophilic; red - hydrophobic) molecular surface is mapped at 1.4 Å (water molecule dimensions) geometrical resolution, for five proteins, from left to right and top to bottom: lysozyme, ribonuclease; hemoglobin; IgG and albumin. The artificial surfaces are as follows: Top left: TEM image (side view) of a defect propagating from layer to layer in otherwise perfectly flat Pt/Rh multi-layered surface; feature: 50×100 Å. Top right: TEM image of gold nanoparticles; features: 10–25 Å. Bottom left: SEM image of a set of SiO<sub>2</sub> pillars with gold caps; features: 150 – 300 Å. Bottom right: SEM image of SiO<sub>2</sub> nano-wires grown from vapor phase; minimum feature: sub-500 Å.</p>", "links"=>[], "tags"=>["proteins", "nano-surfaces"], "article_id"=>652903, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g001", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_surface_of_several_proteins_middle_panel_and_several_artificial_nano_surfaces_and_objects_/652903", "title"=>"Molecular surface of several proteins (middle panel) and several artificial nano-surfaces and objects.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:19:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/988409"], "description"=>"<p>Larger probes (right) cannot visit some inner areas of the protein, as well as some parts of the residues.</p>", "links"=>[], "tags"=>["molecular", "surfaces", "probing", "probe"], "article_id"=>652904, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_of_different_molecular_surfaces_obtained_when_probing_a_protein_with_different_probe_radii_/652904", "title"=>"Schematic of different molecular surfaces obtained when probing a protein with different probe radii.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:19:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/988422"], "description"=>"<p>Comparison presented for all surfaces, i.e., hydrophobic and hydrophilic surfaces (top); hydrophobic surfaces only (middle) and hydrophilic surfaces (bottom). The fitted line in the middle panel represents the linear regression between predicted and observed data, forced to pass through origin, and not the actual multilinear regression with breakpoint best fit</p>", "links"=>[], "tags"=>["piecewise", "linear", "regression", "molecular", "adsorbing", "surfaces", "observed"], "article_id"=>652917, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g009", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_strength_of_the_piecewise_linear_regression_between_molecular_surface_properties_and_concentration_of_protein_on_adsorbing_surfaces_measured_as_the_fit_between_observed_vs_predicted_data_/652917", "title"=>"Statistical strength of the piecewise linear regression between molecular surface properties and concentration of protein on adsorbing surfaces measured as the fit between observed vs. predicted data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:27:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1007283"], "description"=>"<p>Proteins used for the analysis of molecular surfaces.</p>", "links"=>[], "tags"=>["molecular"], "article_id"=>667906, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteins_used_for_the_analysis_of_molecular_surfaces_/667906", "title"=>"Proteins used for the analysis of molecular surfaces.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-14 02:11:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/988417"], "description"=>"<p>Left: Impact of the probe radius on the amphiphilic (a1, top), hydrophobic (a2, second from the top) and hydrophilic (a3, third from the top) densities, i.e., reported to the total area of the protein; and of the hydrophobic (a4, forth from the top) and hydrophilic (a5, fifth from the top) specific densities, i.e., reported to their respective areas for five model proteins: 1LZY  =  lysozyme; 1AFU  =  ribonuclease-A; 1Y4F  =  human hemoglobin; 1AO6  =  human serum albumin; and 1HZH  =  intact human IgG. Right: Impact of the probe radius on the total (b1, top), positive (b2, second from top), and negative (b3, third from top) densities, reported to the total area of the protein; and of positive (b4, forth from top), and negative (b5, fifth from top) specific density, reported to their respective areas for the same five model proteins.</p>", "links"=>[], "tags"=>["hydrophobic", "hydrophilic", "densities", "modulated", "probe"], "article_id"=>652912, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amphiphilic_hydrophobic_and_hydrophilic_densities_and_total_positive_and_negative_densities_modulated_by_the_probe_radius_/652912", "title"=>"Amphiphilic, hydrophobic and hydrophilic densities; and total, positive and negative densities modulated by the probe radius.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:24:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/988411"], "description"=>"<p>Molecular surface area (top) and surface-to-volume (bottom) for five model proteins: 1LZY  =  lysozyme; 1AFU  =  ribonuclease-A; 1Y4F  =  human hemoglobin; 1AO6  =  human serum albumin; and 1HZH  =  intact human IgG.</p>", "links"=>[], "tags"=>["molecular", "surface-to-volume", "radius"], "article_id"=>652906, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g003", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variation_of_the_molecular_surface_area_and_surface_to_volume_ratio_with_the_radius_of_the_probe_/652906", "title"=>"Variation of the molecular surface area and surface-to-volume ratio with the radius of the probe.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:19:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/988427", "https://ndownloader.figshare.com/files/988428", "https://ndownloader.figshare.com/files/988429", "https://ndownloader.figshare.com/files/988442", "https://ndownloader.figshare.com/files/988443"], "description"=>"<div><p>Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.</p> </div>", "links"=>[], "tags"=>["molecular", "mapped", "geometrical", "resolutions"], "article_id"=>652919, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058896.s001", "https://dx.doi.org/10.1371/journal.pone.0058896.s002", "https://dx.doi.org/10.1371/journal.pone.0058896.s003", "https://dx.doi.org/10.1371/journal.pone.0058896.s004", "https://dx.doi.org/10.1371/journal.pone.0058896.s005"], "stats"=>{"downloads"=>20, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Protein_Molecular_Surface_Mapped_at_Different_Geometrical_Resolutions__/652919", "title"=>"Protein Molecular Surface Mapped at Different Geometrical Resolutions", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-15 14:29:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/988420"], "description"=>"<p>Protein properties are bulk amphiphilicity (H_bulk), and amphiphilicity (AA_amph). The adsorbed mass of the respective proteins (as reported in Biomolecular Adsorption Database <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058896#pone.0058896-Vasina1\" target=\"_blank\">[25]</a>). PPMCC calculations are presented for all surfaces (top); hydrophobic (i.e., contact angle > 45°middle); and hydrophilic (i.e., contact angle < 45°bottom).</p>", "links"=>[], "tags"=>["product-moment", "coefficient", "adsorbed"], "article_id"=>652915, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pearson_Product_Moment_Correlation_Coefficient_PPMCC_of_the_relationship_between_protein_parameters_the_protein_adsorbed_mass_/652915", "title"=>"Pearson Product-Moment Correlation Coefficient (PPMCC) of the relationship between protein parameters the protein adsorbed mass.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:26:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/988419"], "description"=>"<p>The top panels represent the ration between the hydrophobic and positive areas, respectively, reported to the hydrophilic and negative areas, respectively. The bottom panels represent the ratios of the respective properties. The members of the sub-set are as follows: 1Y4F (W37A); 1A01 (W37A); 1Y4P (W37E); 1A00 (W37Y); 1Y46 (W37Y); 1Y4G (W37G); 1A0U (V1M); and 1A0Z (V1M).</p>", "links"=>[], "tags"=>["molecular", "single-point", "mutants", "probe"], "article_id"=>652914, "categories"=>["Biochemistry", "Biotechnology", "Biological Sciences", "Chemistry"], "users"=>["Dan V. Nicolau", "Ewa Paszek", "Florin Fulga", "Dan V. Nicolau Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058896.g007", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ratio_of_the_molecular_surface_properties_for_single_point_mutants_haemoglobin_structures_as_a_function_of_the_probe_radius_/652914", "title"=>"Ratio of the molecular surface properties for single-point mutants (haemoglobin structures) as a function of the probe radius.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-15 14:26:04"}

PMC Usage Stats | Further Information

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Relative Metric

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