A Folding Pathway-Dependent Score to Recognize Membrane Proteins
Publication Date
March 01, 2011
Journal
PLOS ONE
Authors
Hamid Hadi Alijanvand, Maryam Rouhani, Elizabeth A. Proctor, Nikolay V. Dokholyan, et al
Volume
6
Issue
3
Pages
e16778
DOI
https://dx.plos.org/10.1371/journal.pone.0016778
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0016778
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21390303
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046963
Europe PMC
http://europepmc.org/abstract/MED/21390303
Scopus
79952292841
Mendeley
http://www.mendeley.com/research/folding-pathwaydependent-score-recognize-membrane-proteins
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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/795325"], "description"=>"<p>To evaluate the FP<sub>3</sub>mem efficiency, we calculated the statistical parameters in various databases. These datasets contain information about transmembrane proteins obtained from x-ray crystallography or other experimental methods used to verify the 3D structure. MPT is the whole MPtopo database. MPT1D and 3D are sub populations of MPT. The m superscripts indicate that the mitochondrial proteins are omitted from the dataset.</p>", "links"=>[], "tags"=>["Computational biology", "cell biology", "biophysics"], "article_id"=>465696, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FP_3_mem_based_statistical_values_for_different_databases_/465696", "title"=>"FP<sub>3</sub>mem-based statistical values for different databases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-01 01:34:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/794874"], "description"=>"<p>A non-linear correlation exists between FP<sub>3</sub>mem and the amount of membrane associations. The FP<sub>3</sub>mem of CN, CNA, CNAA, CNLA1 (APHO 18A3L), CNLA2 (APHO 16A5L), CNLA3 (APHO 14A7L), CNL and CNLL <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016778#pone.0016778-Chen1\" target=\"_blank\">[57]</a> are plotted against the experimentally determined membrane association.</p>", "links"=>[], "tags"=>["membrane"], "article_id"=>465248, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_correlation_between_FP_3_mem_and_the_amount_of_membrane_associations_/465248", "title"=>"The correlation between FP<sub>3</sub>mem and the amount of membrane associations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:27:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/397417", "https://ndownloader.figshare.com/files/397434", "https://ndownloader.figshare.com/files/397454", "https://ndownloader.figshare.com/files/397472", "https://ndownloader.figshare.com/files/397491"], "description"=>"<div><p>While various approaches exist to study protein localization, it is still a challenge to predict where proteins localize. Here, we consider a mechanistic viewpoint for membrane localization. Taking into account the steps for the folding pathway of α-helical membrane proteins and relating biophysical parameters to each of these steps, we create a score capable of predicting the propensity for membrane localization and call it FP<sub>3</sub>mem. This score is driven from the principal component analysis (PCA) of the biophysical parameters related to membrane localization. FP<sub>3</sub>mem allows us to rationalize the colocalization of a number of channel proteins with the Cav1.2 channel by their fewer propensities for membrane localization.</p> </div>", "links"=>[], "tags"=>["folding", "pathway-dependent", "membrane", "proteins"], "article_id"=>138491, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0016778.s001", "https://dx.doi.org/10.1371/journal.pone.0016778.s002", "https://dx.doi.org/10.1371/journal.pone.0016778.s003", "https://dx.doi.org/10.1371/journal.pone.0016778.s004", "https://dx.doi.org/10.1371/journal.pone.0016778.s005"], "stats"=>{"downloads"=>9, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Folding_Pathway_Dependent_Score_to_Recognize_Membrane_Proteins/138491", "title"=>"A Folding Pathway-Dependent Score to Recognize Membrane Proteins", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-01 02:21:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/794753"], "description"=>"<p>Variations of common statistical descriptors (which are used to evaluate a new predictor) in response to the FP<sub>3</sub>mem cut-off changes are depicted. Continues dark line, discontinues line, continues gray line, plus and circle symbol stand for sensitivity, specificity, PPV, accuracy and MCC parameters respectively.</p>", "links"=>[], "tags"=>["dependence", "descriptors"], "article_id"=>465123, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_dependence_of_statistical_descriptors_to_the_FP_3_mem_cut_offs_/465123", "title"=>"The dependence of statistical descriptors to the FP<sub>3</sub>mem cut-offs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:25:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/794262"], "description"=>"<p>The four step-folding pathway of membrane proteins declares the critical factors that play a role in the folding of α-helical membrane proteins. Partitioning includes parameters involved in protein partitioning in the lipid-water interface. The insertion stage contains parameters required for a peptide to insert into plasma membrane. The final folding and association stages indicate critical parameters for the membrane protein folding and packing.</p>", "links"=>[], "tags"=>["helical", "membrane", "folding"], "article_id"=>464628, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alpha_helical_membrane_protein_folding_pathway_/464628", "title"=>"Alpha helical membrane protein folding pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:17:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/795293"], "description"=>"<p>To evaluate the FP<sub>3</sub>mem efficiency, we calculated the statistical parameters for the PSORTb3.0 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016778#pone.0016778-Yu1\" target=\"_blank\">[78]</a> trained sets. PSORTb3.0 is trained on the plasma membrane proteins of prokaryotes selected by searching the SWISSPROT sequence annotations.</p>", "links"=>[], "tags"=>["prokaryotic"], "article_id"=>465666, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FP_3_mem_based_statistical_values_for_a_prokaryotic_dataset_/465666", "title"=>"FP<sub>3</sub>mem-based statistical values for a prokaryotic dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-01 01:34:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/794369"], "description"=>"<p>The changes in parameters that describe the partitioning stage are indicated for bacteria and vertebrate proteins, A) the specific heat capacity, a measure of protein stability, B, C) the specific enthalpy and Gibbs energy of hydration, respectively. D) Free energy change of transfer from water to the POPC interface. Ref. stands for reference proteins. Error bars indicate the SEM for the parameters of each protein. The bar patterns represent Archea: wide upward diagonal, Eubacteria: dashed horizontal, Fishes: horizontal brick, Amphibia: white, Aves: wave, Mammalia: black, APHO 14A7L: black dotted white, APHO 16A5L: white grained black, APHO 18A3L: white dotted black, and APHO: gray dotted white.</p>", "links"=>[], "tags"=>["partitioning"], "article_id"=>464747, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_partitioning_step_parameters_/464747", "title"=>"The partitioning step parameters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:19:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/794626"], "description"=>"<p>The changes in parameters describing the folding and association stages are shown for bacteria and vertebrates proteins. In the A and C panels, the vertical axes are the mean value of the corresponding parameter average for the window that slides along the protein sequence. A) The kProt changes are shown in this panel. kProt is a factor to elucidate α-helix membrane protein topology. B) The specific heat capacity of hydration for the channels, references and actinin is shown in this board. ΔCp(hyd) points out the hydrophobic patches. C) The occurrence number of the GG4Br motif in windows is defined as a scale for helix packing. Ref. stands for the reference proteins. The error bars indicate the SEM for the parameters of each protein. The bar patterns represent Archea: wide upward diagonal, Eubacteria: dashed horizontal, Fishes: horizontal brick, Amphibia: white, Aves: wave, Mammalia: black, APHO 14A7L: black dotted white, APHO 16A5L: white grained black, APHO 18A3L: white dotted black, and APHO: gray dotted white.</p>", "links"=>[], "tags"=>["folding", "stages"], "article_id"=>464995, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_folding_and_association_stages_parameters_/464995", "title"=>"The folding and association stages parameters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:23:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/794470"], "description"=>"<p>The changes in parameters describing the insertion stage are shown for bacterial and vertebrate proteins. The vertical axes are the mean value of the corresponding parameter average for the window that slides along the protein sequence. A) The variation of ΔG(oct) is illustrated, which is a whole residue hydrophobicity scale and a sign of the protein membrane propensity. B) The alpha helix propensity is a measure of the tendency to form alpha helix, which is characterized by ΔΔG(α-helix). Ref. stands for the reference proteins. The error bars indicate the SEM for the parameters of each protein. The bar patterns represent Archea: wide upward diagonal, Eubacteria: dashed horizontal, Fishes: horizontal brick, Amphibia: white, Aves: wave, Mammalia: black, APHO 14A7L: black dotted white, APHO 16A5L: white grained black, APHO 18A3L: white dotted black, and APHO: gray dotted white.</p>", "links"=>[], "tags"=>["insertion"], "article_id"=>464842, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_insertion_step_parameters_/464842", "title"=>"The insertion step parameters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:20:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/795157"], "description"=>"<p>Many membrane proteins co-localize with the Ca<sub>v</sub> channel. The FP<sub>3</sub>mem values of those proteins are compared with the Ca<sub>v</sub> FP<sub>3</sub>mem. The FP<sub>3</sub>mem cut-off value for the plasma membrane proteins is set at −31. The average FP<sub>3</sub>mem for the transmembrane proteins of Archea, Bacteria, and Eukaryotes are retrieved from Uniprot and presented for comparison. The error bars indicate the SEM.</p>", "links"=>[], "tags"=>["nmdar", "co-localize"], "article_id"=>465526, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AMPAR_and_NMDAR_co_localize_with_the_Ca_v_channel_/465526", "title"=>"AMPAR and NMDAR co-localize with the Ca<sub>v</sub> channel.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:32:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/795266"], "description"=>"<p>To evaluate the FP<sub>3</sub>mem efficiency, we calculated the statistical parameters for the eSLDB <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016778#pone.0016778-Pierleoni1\" target=\"_blank\">[79]</a>. This database contains the whole proteome of many eukaryotes. FP<sub>3</sub>mem identifies the transmembrane proteins of human, yeast and nematode from the database with the indicated efficiencies.</p>", "links"=>[], "tags"=>["eukaryotic"], "article_id"=>465636, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FP_3_mem_based_statistical_values_for_a_eukaryotic_dataset_/465636", "title"=>"FP<sub>3</sub>mem-based statistical values for a eukaryotic dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-01 01:33:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/795026"], "description"=>"<p>Columns indicate the FP<sub>3</sub>mem value for each protein over evolutionary time. The mammalian columns are colored gray for an easier comparison. The error bars designate the SEM.</p>", "links"=>[], "tags"=>["Computational biology", "cell biology", "biophysics"], "article_id"=>465394, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.g007", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_FP_3_mem_values_of_rSKs_945_actinin_and_Ca_v_1_2_proteins_/465394", "title"=>"The FP<sub>3</sub>mem values of rSKs, α-actinin and Ca<sub>v</sub>1.2 proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-01 01:29:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/795357"], "description"=>"<p>The FP<sub>3</sub>mem efficiency is compared with other methods on the same datasets that are common for predicting protein membrane localization. Sen and Spe are the abbreviation of sensitivity and specificity respectively.</p>", "links"=>[], "tags"=>["Computational biology", "cell biology", "biophysics"], "article_id"=>465727, "categories"=>["Biological Sciences", "Cell Biology", "Biophysics"], "users"=>["Hamid Hadi-Alijanvand", "Maryam Rouhani", "Elizabeth A. Proctor", "Nikolay V. Dokholyan", "Ali A. Moosavi-Movahedi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016778.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_FP_3_mem_efficiency_with_other_methods_/465727", "title"=>"Comparison of the FP<sub>3</sub>mem efficiency with other methods.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-01 01:35:27"}

PMC Usage Stats | Further Information

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