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PMAP: databases for analyzing proteolytic events and pathways

Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak (+4 others)
2008 Nucleic Acids Research  
Here, we describe how the databases of PMAP can be used to foster understanding of proteolytic pathways, and equally as significant, to reason about proteolysis.  ...  PMAP also contains two community annotated databases focused on function; CutDB has information on more than 5000 proteolytic events, and ProfileDB is dedicated to information of the substrate recognition  ...  ACKNOWLEDGEMENTS We thank many at the Burnham Institute for Medical Research for the data curation and Dr Weizhong Li for providing protein annotation pipeline.  ... 
doi:10.1093/nar/gkn683 pmid:18842634 pmcid:PMC2686432 fatcat:kp24qbe6vjhmfdsqvhhswibbcu

Sequence-derived structural features driving proteolytic processing

Alexander A. Belushkin, Dmitry V. Vinogradov, Mikhail S. Gelfand, Andrei L. Osterman, Piotr Cieplak, Marat D. Kazanov
2013 Proteomics  
Proteolytic signaling, or regulated proteolysis, is an essential part of many important pathways such as Notch, Wnt, and Hedgehog.  ...  Here, we analyzed the relative importance in proteolysis of various structural features derived from substrate sequences using a dataset of more than five thousand experimentally verified proteolytic events  ...  Acknowledgments We would like to thank Yoshinobu Igarashi, Boris Ratnikov, Alexey Eroshkin, and Jeff Smith for useful discussions.  ... 
doi:10.1002/pmic.201300416 pmid:24227478 pmcid:PMC3926948 fatcat:hambphxqk5hsjheaeewmajwkre

Proteolytic Post-translational Modification of Proteins: Proteomic Tools and Methodology

Lindsay D. Rogers, Christopher M. Overall
2013 Molecular & Cellular Proteomics  
these fields enabling in vivo analysis of proteolytic events.  ...  Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease.  ...  CutDB is part of the larger PMAP website, which also contains protease and substrate databases and tools for determining protease specificities and mapping signaling pathways (73) .  ... 
doi:10.1074/mcp.m113.031310 pmid:23887885 pmcid:PMC3861706 fatcat:wp4o5og5bnecxpxawdp2tveqa4

Profiling protease activities by dynamic proteomics workflows

Diana Klingler, Markus Hardt
2012 Proteomics  
defining in vitro and in vivo proteolytic events.  ...  Recently, activity-based workflows have come to the forefront to tackle the dynamic aspects of proteolytic processing networks in vitro, ex vivo and in vivo.  ...  Acknowledgments This work was partially supported by a grant from the National Institute of Dental and Craniofacial Research (R01 DE 019796) to Markus Hardt.  ... 
doi:10.1002/pmic.201100399 pmid:22246865 pmcid:PMC3431026 fatcat:p5bsupjguvgmthjmkp3rkjcbjm


2011 Journal of Bioinformatics and Computational Biology  
We discuss the advantages and drawbacks of the current methods and detail how more accurate models can be built by deriving multiple sequence and structural features of substrates.  ...  Song et al. protease substrate cleavage sites and identifying novel putative substrates.  ...  proteins in vivo or in vitro; PMAP, 74 an integrated database for analyzing proteolytic events and pathways; and the Degradome database, 75 which assembles all of the relevant mammalian proteases and  ... 
doi:10.1142/s0219720011005288 pmid:21328711 fatcat:57qircygovbura43rsql2q7mjq

A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome

Michał Kistowski, Janusz Dębski, Jakub Karczmarski, Agnieszka Paziewska, Jacek Olędzki, Michał Mikula, Jerzy Ostrowski, Michał Dadlez
2016 Molecular & Cellular Proteomics  
During the course of peptide-wise analysis of shotgun proteomic datasets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed  ...  Proteolytic cascades are deeply involved in critical stages of cancer progression.  ...  We analyzed all cleavage sites within the MEROPS (28) and PMAP-CutDB (29) databases to find proteases characterized by the P1 VIATC consensus and lack of preferences at other positions.  ... 
doi:10.1074/mcp.m116.058818 pmid:27927741 pmcid:PMC5294209 fatcat:pb4gqdrrnnfiriwtuhtvfx4pda

Measuring Apoptosis: Caspase Inhibitors and Activity Assays

G. P. McStay, D. R. Green
2014 Cold Spring Harbor Protocols  
Many of these techniques use molecules that are based on optimal peptide motifs for each caspase and on our understanding of caspase cleavage events that occur during apoptosis.  ...  Recently, probes having greater specificity for individual caspases have been developed and are being used successfully.  ...  Belizario for further information. b A large protease and substrate database with large amounts of information on caspases and substrates from many species.  ... 
doi:10.1101/pdb.top070359 pmid:25086023 fatcat:ozdhhar2hvfhzg27xh5sfd6kj4

Early infiltration of p40IL12+CCR7+CD11b+cells is critical for fibrosis development

Tarcio Teodoro Braga, Matheus Correa-Costa, Hatylas Azevedo, Reinaldo Correia Silva, Mario Costa Cruz, Maira Estanislau Soares Almeida, Meire Ioshie Hiyane, Carlos Alberto Moreira-Filho, Marinilce Fagundes Santos, Katia Regina Perez, Iolanda Midea Cuccovia, Niels Olsen Saraiva Camara
2016 Immunity, Inflammation and Disease  
The injection of M (IFNg þ LPS) cells was associated with the up-regulation of inflammation-and fibrosis-related proteins (Thbs1, Mmp7, Mmp8, and Mmp13).  ...  We observed a similar profile after injection of sorted CCR7 þ CD11b þ cells and a more pronounced effect of M (IFNg þ LPS) cells originated from Stat6 À/À mice.  ...  With this interaction profile data, proteolytic networks were constructed to analyze proteolytic profiles and pathways specific to each macrophage subtype.  ... 
doi:10.1002/iid3.114 pmid:27621813 pmcid:PMC5004285 fatcat:vvtbpve6ijcktbrrkmpuuadacy

The Dendritic Cell Major Histocompatibility Complex II (MHC II) Peptidome Derives from a Variety of Processing Pathways and Includes Peptides with a Broad Spectrum of HLA-DM Sensitivity

Cristina C. Clement, Aniuska Becerra, Liusong Yin, Valerio Zolla, Liling Huang, Simone Merlin, Antonia Follenzi, Scott A. Shaffer, Lawrence J. Stern, Laura Santambrogio
2016 Journal of Biological Chemistry  
Although intracellular endosomal processing in dendritic cells and B cells has been characterized for a few antigens, the overall range of processing pathways responsible for generating the MHC II peptidome  ...  The processing enzymes were identified by reference to a database of experimentally determined cleavage sites and experimentally validated for four epitopes derived from complement 3, collagen II, thymosin  ...  The MEROPS database (58) was searched in combination with the PMAP CutDB proteolytic events database (59) to assign the proteases families responsible for the generation of the N-and C-terminal cleavage  ... 
doi:10.1074/jbc.m115.655738 pmid:26740625 pmcid:PMC4786700 fatcat:cgz2yzfvtbbdneqbsxcu2ey4qi

PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

Jiangning Song, Hao Tan, Andrew J. Perry, Tatsuya Akutsu, Geoffrey I. Webb, James C. Whisstock, Robert N. Pike, Narayanaswamy Srinivasan
2012 PLoS ONE  
To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases.  ...  Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage  ...  of proteolytic pathways.  ... 
doi:10.1371/journal.pone.0050300 pmid:23209700 pmcid:PMC3510211 fatcat:6azihz6ntvc7jolw4mqb7wi55m

Rheumatic Heart Disease and Myxomatous Degeneration: Differences and Similarities of Valve Damage Resulting from Autoimmune Reactions and Matrix Disorganization

Carlo de Oliveira Martins, Lea Demarchi, Frederico Moraes Ferreira, Pablo Maria Alberto Pomerantzeff, Carlos Brandao, Roney Orismar Sampaio, Guilherme Sobreira Spina, Jorge Kalil, Edecio Cunha-Neto, Luiza Guilherme, Katherine Yutzey
2017 PLoS ONE  
Confocal microscopy analysis revealed a diverse pattern of distribution of collagen VI and lumican into RHD and MXD valves.  ...  We also found increased vitronectin expression, reduced collagen VI expression and similar lumican expression between RHD and MXD valves.  ...  Acknowledgments We thank Prof Francisco Laurindo from the Heart Institute (InCor), Clinical Hospital University of São Paulo, for a critical review of this manuscript and Ms Ana Lucia Garippo also from  ... 
doi:10.1371/journal.pone.0170191 pmid:28121998 pmcid:PMC5266332 fatcat:4cqp7cuyrfahnap42ms6e7vilm

The C-Terminal Fragment of Prostate-Specific Antigen, a 2331 Da Peptide, as a New Urinary Pathognomonic Biomarker Candidate for Diagnosing Prostate Cancer

Kenji Nakayama, Takahiro Inoue, Sadanori Sekiya, Naoki Terada, Yu Miyazaki, Takayuki Goto, Shigeki Kajihara, Shin-Ichiro Kawabata, Shinichi Iwamoto, Kuniko Ikawa, Junko Oosaga, Hiroaki Tsuji (+3 others)
2014 PLoS ONE  
Therefore, the aim of this study was to discover new biomarkers for the diagnosis of PCa.  ...  and Objectives: Prostate cancer (PCa) is one of the most common cancers and leading cause of cancer-related deaths in men.  ...  Taka-Aki Sato, Minoru Suzuki, and Hiroki Kuyama at Koichi Tanaka Laboratory of Advanced Science and Technology of Shimadzu Corporation for their helpful support and advice.  ... 
doi:10.1371/journal.pone.0107234 pmid:25233230 pmcid:PMC4169392 fatcat:mx7c34t7yzho5nkvd3lfpfwspy


2019 Seibutsu Butsuri  
Here, we performed CMDs with various cosolvent molecules and analyzed the correlation between the cosolvent structure and the Pmap.  ...  pathway of ADRB2.  ...  Kinesin is a motor protein that uses microtubules as pathways for intracellular transport.  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

Molekuliarno-strukturnaia gomologiia proteoliticheskikh fermentov [chapter]
Молекулярно-структурная гомология протеолитических ферментов

Aleksandr Aleksandrovich Chirkin, A. A. Balaeva-Tikhomirova
2022 Molecular-structural Homology of Proteolytic Enzymes  
Публикация: "PMAP": databases for analyzing proteolytic events and pathways". Nucleic Acids Research. 37: D611-D618. Базу можно найти по адресу, представленному в Wikipedia: doi: 10.1093/nar/gkn683.  ...  OECD Environment, Health and Safety Publications. Series on testing and assessment. -Paris: Environment directorate organization for economic co-operation and development, 2010. -№121. -182 p.».  ... 
doi:10.31483/r-100736 fatcat:nwugx722vfdwxhkeavska66wma

New Antimicrobials Project 2 nd Workshop New Compounds & New Strategies for

Antimicrobials, William Shafer
2012 unpublished
The more conserved of these can be used for searching cDNA, UniProtKB or other protein databases for novel bioactive peptides, for creating PROSITE search patterns, and for phylogenetic analysis.  ...  database queries.  ...  All experiments were compared with liposome-leakage measurements: while for PMAP-23 all membraneperturbing effects are correlated with the vesicle leakage process, alamethicin does not significantly influence  ... 
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