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• {"link"=>{"url"=>"http://www.citeulike.org/user/jjray/article/13326636"}, "post_time"=>"2014-08-29 15:46:17", "tag"=>["enzyme", "kinetics", "memory"], "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pcbi.1003784"}, "username"=>"jjray", "article_id"=>"13326636"}
• {"link"=>{"url"=>"http://www.citeulike.org/user/kinop/article/13326636"}, "post_time"=>"2014-08-15 04:19:51", "tag"=>"biological-network", "linkout"=>{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pcbi.1003784"}, "username"=>"kinop", "article_id"=>"13326636"}

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{"title"=>"Kinetic Memory Based on the Enzyme-Limited Competition", "type"=>"journal", "authors"=>[{"first_name"=>"Tetsuhiro S.", "last_name"=>"Hatakeyama", "scopus_author_id"=>"54400905300"}, {"first_name"=>"Kunihiko", "last_name"=>"Kaneko", "scopus_author_id"=>"7403696146"}], "year"=>2014, "source"=>"PLoS Computational Biology", "identifiers"=>{"pui"=>"607917011", "sgr"=>"84927976278", "issn"=>"15537358", "pmid"=>"25121967", "scopus"=>"2-s2.0-84927976278", "doi"=>"10.1371/journal.pcbi.1003784", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)"}, "id"=>"8c29cbae-b472-3f74-b556-8fe8886ecf86", "abstract"=>"Cellular memory, which allows cells to retain information from their environment, is important for a variety of cellular functions, such as adaptation to external stimuli, cell differentiation, and synaptic plasticity. Although posttranslational modifications have received much attention as a source of cellular memory, the mechanisms directing such alterations have not been fully uncovered. It may be possible to embed memory in multiple stable states in dynamical systems governing modifications. However, several experiments on modifications of proteins suggest long-term relaxation depending on experienced external conditions, without explicit switches over multi-stable states. As an alternative to a multistability memory scheme, we propose \"kinetic memory\" for epigenetic cellular memory, in which memory is stored as a slow-relaxation process far from a stable fixed state. Information from previous environmental exposure is retained as the long-term maintenance of a cellular state, rather than switches over fixed states. To demonstrate this kinetic memory, we study several models in which multimeric proteins undergo catalytic modifications (e.g., phosphorylation and methylation), and find that a slow relaxation process of the modification state, logarithmic in time, appears when the concentration of a catalyst (enzyme) involved in the modification reactions is lower than that of the substrates. Sharp transitions from a normal fast-relaxation phase into this slow-relaxation phase are revealed, and explained by enzyme-limited competition among modification reactions. The slow-relaxation process is confirmed by simulations of several models of catalytic reactions of protein modifications, and it enables the memorization of external stimuli, as its time course depends crucially on the history of the stimuli. This kinetic memory provides novel insight into a broad class of cellular memory and functions. In particular, applications for long-term potentiation are discussed, including dynamic modifications of calcium-calmodulin kinase II and cAMP-response element-binding protein essential for synaptic plasticity.", "link"=>"http://www.mendeley.com/research/kinetic-memory-based-enzymelimited-competition-1", "reader_count"=>14, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>1, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>1, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>1, "Agricultural and Biological Sciences"=>5, "Physics and Astronomy"=>4}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>3}, "group_count"=>0}

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• http://doi.org/10.1371/journal.pgen.1007744
• http://doi.org/10.1371/journal.pcbi.1005847
• http://doi.org/10.1073/pnas.1615351114
• http://doi.org/10.1088/1751-8121/aa54e3
• http://doi.org/10.1371/journal.pcbi.1005434
• http://doi.org/10.1016/j.bpj.2016.07.036

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• {"id"=>"501729039162150913", "text"=>"Kinetic memory is easily affected by continuous changes in external stimuli: http://t.co/G1zUOl3TLg", "created_at"=>"2014-08-19T13:54:59Z", "user"=>"PLOSCompBiol", "user_name"=>"PLOS Comp Biol", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2435436417/hg8nh61i55aibgx0hcvp_normal.jpeg"}
• {"id"=>"501897328639639552", "text"=>"RT @PLOSCompBiol: Kinetic memory is easily affected by continuous changes in external stimuli: http://t.co/G1zUOl3TLg", "created_at"=>"2014-08-20T01:03:42Z", "user"=>"apuertag", "user_name"=>"Andrés Puertag", "user_profile_image"=>"http://pbs.twimg.com/profile_images/456480141170851840/cPt49EXq_normal.jpeg"}
• {"id"=>"505375328517107712", "text"=>"Kinetic Memory Based on the Enzyme-Limited Competition - http://t.co/FqBxxwDgYz #science #biochemistry #biology #mind #brain", "created_at"=>"2014-08-29T15:24:02Z", "user"=>"rlanzara", "user_name"=>"Richard G. Lanzara", "user_profile_image"=>"http://pbs.twimg.com/profile_images/89594702/MyPict2_normal.jpg"}
• {"id"=>"505375992945598464", "text"=>"RT @rlanzara: Kinetic Memory Based on the Enzyme-Limited Competition - http://t.co/FqBxxwDgYz #science #biochemistry #biology #mind #brain", "created_at"=>"2014-08-29T15:26:40Z", "user"=>"sciencestream", "user_name"=>"Science Stream", "user_profile_image"=>"http://pbs.twimg.com/profile_images/1825311976/rss_logo_normal.gif"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1635703"], "description"=>"<p>Schematic representation (A) and reaction diagram (B) of our model. A substrate has modification sites. Modification reactions for the substrates progress without catalyst at rates and demodification reactions are facilitated by the catalyst at rates .</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139113, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_reaction_scheme_of_the_chained_modification_model_/1139113", "title"=>"The reaction scheme of the chained modification model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635704"], "description"=>"<p>The initial condition is set as and for other , and the relaxation process of the modification level is computed without input (). The parameters are given as , , and . The time courses for the modification level for different values of the catalyst concentration, , , , , , , , , and , are plotted with different colors, where the concentration of is fixed at . Although exponential relaxation is observed as in first-order reactions (dotted line) when the concentration of the catalyst is sufficiently large, the relaxation is drastically slowed as the concentration of the catalyst becomes lower than that of the substrate.</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139114, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Slow_logarithmic_relaxation_of_the_chained_modification_model_/1139114", "title"=>"Slow logarithmic relaxation of the chained modification model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635705"], "description"=>"<p> is plotted against ; is defined as the time when the summation of all of falls below the threshold value() without input, starting from the initial condition (). (A) , , . (B) , , . (C) , , .</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139115, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Change_in_the_dependence_of_the_catalyst_on_the_relaxation_time_against_the_dissociation_constant_A_against_the_heterogeneity_of_the_dissociation_constant_B_and_against_the_number_of_modification_sites_C_/1139115", "title"=>"Change in the dependence of the catalyst on the relaxation time against , the dissociation constant (A), against , the heterogeneity of the dissociation constant (B), and against , the number of modification sites (C).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635706"], "description"=>"<p>The time course of for each is plotted by setting the initial conditions as already described. (A) 's relax in descending order, in the same manner as in the first-order reactions. (B) 's relax in ascending order, that is, converse to the order expected from the first-order reactions. The highly modified state relaxes only after the relaxation of the less-modified . The relaxation process consists of several plateaus, which are typically observed in the relaxation process of kinetic glass <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003784#pcbi.1003784-AwazuAKaneko1\" target=\"_blank\">[25]</a>.</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139116, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g004", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relaxation_process_of_each_/1139116", "title"=>"Relaxation process of each .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635707"], "description"=>"<p>(A) The relaxation time after exposure to the stimulus with various magnitudes and durations is plotted as a color map. The initial condition is given as and for , and the input is given as for and for . When the magnitude () and duration of the stimulus () increase, increases continuously over an order of magnitude. The catalyst concentration is set at of the substrate concentration. (B) Dependence of the relaxation process on the duration of stimulus exposure. The duration of stimulus exposure is changed while the magnitude is fixed at . Here, the relaxation time increases nearly exponentially with the increase in duration for the some extent small . When is sufficiently long, the modification is maintained for a long time.</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139117, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g005", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dependence_of_the_relaxation_process_on_the_magnitude_and_duration_of_a_stimulus_/1139117", "title"=>"Dependence of the relaxation process on the magnitude and duration of a stimulus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635708"], "description"=>"<p>The relaxation times of the variables are plotted against the total concentration of phosphatase. is defined as the time when the summation of of all falls below the threshold value, after relaxation at a kinase-rich condition (). The model shows the transition from fast exponential relaxation to slow logarithmic relaxation at the critical point (). (When the amount of the phosphatase is lower than that of kinase (), the relaxation time itself is shorter, whereas the logarithmic relaxation remains. Here, the stable fixed-point value of the concentration changes to a higher value, and the relaxation time is decreased.)</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139118, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g006", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kinase_phosphatase_model_A_and_its_relaxation_time_B_/1139118", "title"=>"Kinase-phosphatase model (A) and its relaxation time (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635709"], "description"=>"<p>After the system is relaxed in the presence of the attractant as , the system transitions to a repellant condition as , and the relaxation process of is computed. The parameters are given as , , and . The time courses of for different values of the catalyst concentration, , , , , , , , , and , are plotted with different colors, where the concentration of is fixed at . Although exponential relaxation is observed as in the original A-H model (dotted line), when the concentration of the catalyst is sufficiently large, the relaxation is drastically slowed as the concentration of the catalyst becomes lower than that of the substrate.</p>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139119, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003784.g007", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_extended_Asakura_Honda_model_A_and_its_slow_logarithmic_relaxation_after_exposure_to_an_environmental_stimulus_B_/1139119", "title"=>"The extended Asakura-Honda model (A) and its slow logarithmic relaxation after exposure to an environmental stimulus (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-14 09:11:41"}
• {"files"=>["https://ndownloader.figshare.com/files/1635710", "https://ndownloader.figshare.com/files/1635711", "https://ndownloader.figshare.com/files/1635712", "https://ndownloader.figshare.com/files/1635713", "https://ndownloader.figshare.com/files/1635714", "https://ndownloader.figshare.com/files/1635715", "https://ndownloader.figshare.com/files/1635716", "https://ndownloader.figshare.com/files/1635717"], "description"=>"<div><p>Cellular memory, which allows cells to retain information from their environment, is important for a variety of cellular functions, such as adaptation to external stimuli, cell differentiation, and synaptic plasticity. Although posttranslational modifications have received much attention as a source of cellular memory, the mechanisms directing such alterations have not been fully uncovered. It may be possible to embed memory in multiple stable states in dynamical systems governing modifications. However, several experiments on modifications of proteins suggest long-term relaxation depending on experienced external conditions, without explicit switches over multi-stable states. As an alternative to a multistability memory scheme, we propose “kinetic memory” for epigenetic cellular memory, in which memory is stored as a slow-relaxation process far from a stable fixed state. Information from previous environmental exposure is retained as the long-term maintenance of a cellular state, rather than switches over fixed states. To demonstrate this kinetic memory, we study several models in which multimeric proteins undergo catalytic modifications (e.g., phosphorylation and methylation), and find that a slow relaxation process of the modification state, logarithmic in time, appears when the concentration of a catalyst (enzyme) involved in the modification reactions is lower than that of the substrates. Sharp transitions from a normal fast-relaxation phase into this slow-relaxation phase are revealed, and explained by enzyme-limited competition among modification reactions. The slow-relaxation process is confirmed by simulations of several models of catalytic reactions of protein modifications, and it enables the memorization of external stimuli, as its time course depends crucially on the history of the stimuli. This kinetic memory provides novel insight into a broad class of cellular memory and functions. In particular, applications for long-term potentiation are discussed, including dynamic modifications of calcium-calmodulin kinase II and cAMP-response element-binding protein essential for synaptic plasticity.</p></div>", "links"=>[], "tags"=>["modification reactions", "Synaptic plasticity", "protein", "multistability memory scheme", "ii"], "article_id"=>1139120, "categories"=>["Biological Sciences"], "users"=>["Tetsuhiro S. Hatakeyama", "Kunihiko Kaneko"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003784.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s003", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s004", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s005", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s006", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s007", "https://dx.doi.org/10.1371/journal.pcbi.1003784.s008"], "stats"=>{"downloads"=>11, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kinetic_Memory_Based_on_the_Enzyme_Limited_Competition_/1139120", "title"=>"Kinetic Memory Based on the Enzyme-Limited Competition", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-14 09:11:41"}

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Relative Metric

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