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K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores

Arnold I Emerson, Simeon Andrews, Ikhlak Ahmed, Thasni Azis, Joel A Malek
2015 Journal of Clinical Bioinformatics  
This study provides evidence that a majority of protein domains in the inner core of the DCN have a lower mutation frequency and that protein domains present in the peripheral regions of the k-core contribute  ...  Mutations and domain co-occurrence networks provide a framework for understanding hierarchal designs in protein function from a network perspective.  ...  K-core decomposition of DCN To identify the core-periphery organization of the domain co-occurrence network, we subjected it to core decomposition.  ... 
doi:10.1186/s13336-015-0016-6 pmid:25767694 pmcid:PMC4357223 fatcat:iq6uiqku5rc6pdlvatwj6eelja

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

Fabian Fröhlich, Thomas Kessler, Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache, Artur Muradyan, Moritz Schütte, Ji-Hyun Lim, Matthias Heinig, Fabian J. Theis, Hans Lehrach (+3 others)
2018 Cell Systems  
Here, we present a computational framework for the parameterization of large-scale mechanistic models and its application to the prediction of drug response of cancer cell lines from exome and transcriptome  ...  KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360.  ...  To obtain a model for a particular cancer cell line, we individualized the mechanistic model by incorporating gene expression levels as synthesis rates for proteins and their mutated functional variants  ... 
doi:10.1016/j.cels.2018.10.013 fatcat:on4fgrx5ofhs5cuzann4hufc6y

Award Winners and Abstracts of the 31st Annual Symposium of The Protein Society, Montreal, Canada, July 24-27, 2017

2017 Protein Science  
In the present study, we aimed to improve the ExM method for imaging of proteins in human clinical tissue samples, for diagnostic pathology and research.  ...  RESULTS and CONCLUSIONS: This ExPath protocol enabled expansion of human normal and cancer tissues $4.5x in linear dimension and $100x in volume, with a post-expansion measurement error of <5%.  ...  Relative frequency of occurrence F_ijkl was calculated for each atomic quadruplet type (i,j,k,l) using the observed tetrahedra, and rate P_ijkl expected by chance was determined from a multinomial reference  ... 
doi:10.1002/pro.3349 pmid:29280217 fatcat:jrxtwzblare37gxsvc5szbwuhu

Leukocyte-Endothelial Cell Adhesion Molecule 2 (LECAM2) [chapter]

2017 Encyclopedia of Cancer  
this cationic peptide on a broad range of cancer cell types, including leukemias, lymphomas, fibrosarcomas, and various carcinomas.  ...  A similar, but less potent, antiangiogenic activity has also been reported for bovine lactoferrin.  ...  References Agrawal N, Kango M, Mishra A, Sinha P (1995) Neoplastic transformation and aberrant cell-cell interactions in genetic mosaics of lethal (2)  ... 
doi:10.1007/978-3-662-46875-3_101347 fatcat:wq4gqlizr5csfjlwv4opja2jb4

Forty-First Annual Meeting March 2-6, 1997 Ernest N. Morial Convention Center New Orleans, Louisiana. Monday Symposia and Posters, Part I

1997 Biophysical Journal  
The influence of temperature on the rate of cross-bridge cycling and tension development was studied in cardiac trabeculae isolated from rat hearts.  ...  ATPase activity was measured on-line by an enzyme coupled NADH absorbance assay and A expressed per fiber volume. Force development was studied over a  ...  Yet they take place in the densely packed interior of proteins.  ... 
doi:10.1016/s0006-3495(97)78732-0 fatcat:mrn7bn5kzrcp3bd7zvhmod6pcy

Magnetic Nanoparticle Composites: Synergistic Effects and Applications

Stefanos Mourdikoudis, Athanasia Kostopoulou, Alec P. LaGrow
2021 Advanced Science  
Common types of nanocomposites consist of a combination of two different elements, with a nanoparticle that is linked to, or surrounded by, another organic or inorganic material, for example in a core-shell  ...  A general family of nanoparticle composites concerns the coating of a nanoscale material by a polymer, SiO2 or carbon.  ...  The authors thank the UCL Open Access Team for covering the article processing charges. Conflict of Interest The authors declare no conflict of interest.  ... 
doi:10.1002/advs.202004951 pmid:34194936 pmcid:PMC8224446 fatcat:bsdh6jcsxfdxndxfqawnjxkj4u

IAF [chapter]

Michel Viso
2015 Encyclopedia of Astrobiology  
IRAS also revealed for the first time the core of our galaxy, the Milky Way.  ...  For indirect effects, the number of changed molecules increases with increasing ▶ linear energy transfer (LET). ▶ Mutations, cancer induction, and cell death are the most critical biological radiation  ...  of H 2 D + , and k M is the rate coefficient for reaction of H 2 D + with neutral species M.  ... 
doi:10.1007/978-3-662-44185-5_1779 fatcat:p5uzlccrjjartj37w2d4bkgima

Leukemia Inhibitory Factor [chapter]

Mariusz Z. Ratajczak
2011 Encyclopedia of Cancer  
A et al (2006) The LIM domain protein LPP is a coactivator for the ETS domain transcription factor PEA3.  ...  lower than that for white men Prospective studies demonstrated a rising trend in lung cancer death rates with the duration and intensity of smoking.  ...  An understanding of the molecular mechanisms that regulate lymphangiogenesis may lead to new therapies for cancer metastasis and lymphedema.  ... 
doi:10.1007/978-3-642-16483-5_3324 fatcat:zidjhru75rb5fc7wwmjjuriqkq

Superoxide Dismutases and Superoxide Reductases

Yuewei Sheng, Isabel A. Abreu, Diane E. Cabelli, Michael J. Maroney, Anne-Frances Miller, Miguel Teixeira, Joan Selverstone Valentine
2014 Chemical Reviews  
of this mutation in a variety of diseases (e.g., cancer, cardiovascular disease).  ...  the SOD1 protein in the core of the amyloid fibril. 329 6.6.2.  ... 
doi:10.1021/cr4005296 pmid:24684599 pmcid:PMC4317059 fatcat:u5d7jdnk2jb7zdriv4esmowsdq

第57回年会予稿集

2019 Seibutsu Butsuri  
The negative correlation retained after controlling for non-random mutation rate, suggesting a constraint by purifying selection rather than any constraint of mutation rate. 1Pos239 (1SEA-5) Molecular  ...  co-receptors in the regulation of cancer immunity as well as autoimmunity.  ...  Kinesin is a motor protein that uses microtubules as pathways for intracellular transport.  ... 
doi:10.2142/biophys.59.s1 fatcat:rsudhlmaanetrhmdxjgsiyorme

Poster Sessions

2003 Analytical Cellular Pathology  
During megakaryocytic differentiation of K-562 cells we determined down regulation of chimeric Bcr/Abl genes and co-localization of studied loci with mH3 (K4) regions was not observed.  ...  Introduction: Prostate cancer is the second leading cause of cancer death in men. A major prerequisite for tumor initiation and progression is the acquisition of chromosomal aberrations.  ...  The full-length gene encodes a mature protein of 282 amino acids, predicted to have a single transmembrane domain.  ... 
doi:10.1155/2003/698262 fatcat:5los6z723begbf4srdwa5cu6wm

Forty-First Annual Meeting March 2–6, 1997 Ernest N. Morial Convention Center New Orleans, Louisiana

1997 Biophysical Journal  
In the SBLM the critical voltage for imstability, Vj,(k), is k-sensitive. For V I < VJ,(0), the ESM is always stable but the SBLM may be unstable.  ...  J., 13, 711 [1973]), a limiting case of the SBLM, instability is not k dependent and is preceded by large membrane electrostriction.  ...  Specificity Is conferred by a network of direct and water mediated protein-DNA hydrogen bonds.  ... 
doi:10.1016/s0006-3495(97)78735-6 fatcat:fwfbe5dox5hunpzqz2y2qfckwi

Copper Active Sites in Biology

Edward I. Solomon, David E. Heppner, Esther M. Johnston, Jake W. Ginsbach, Jordi Cirera, Munzarin Qayyum, Matthew T. Kieber-Emmons, Christian H. Kjaergaard, Ryan G. Hadt, Li Tian
2014 Chemical Reviews  
The latter is formed in a biogenesis reaction of a residue (Tyr) that is also Cu catalyzed in the first turnover of the protein.  ...  Copper sites that perform ET are the mononuclear blue Cu site that has a highly covalent Cu II -S(Cys) bond and the binuclear Cu A site that has a Cu 2 S(Cys) 2 core with a Cu-Cu bond that keeps the site  ...  Ryan Cowley for thoughtful comments. The funding for this research by NIH grant DK31450 is gratefully acknowledged.  ... 
doi:10.1021/cr400327t pmid:24588098 pmcid:PMC4040215 fatcat:jmntpve4mbad3kbupdtmjcftom

Bio-inorganic chemistry

Andrew J Thomson, Harry B Gray
1998 Current Opinion in Chemical Biology  
We thank them for their contributions. Even with all this help, the book would never have seen the light of day had it not been for the dedication and hard work of Debbie Wuttke.  ...  vii viii Acknowledgments The idea of preparing a bioinorganic chemistry textbook was conceived by one of us (IB) at a "Metals in Biology" Gordon Conference in January, 1986.  ...  P. k_ 1 Approximated as the reciprocal ratio between on-and off-rate constants relevant to the solute-protein complex, lIK m = k]/k_] may be taken as a lower limit of the affinity of the protein for the  ... 
doi:10.1016/s1367-5931(98)80056-2 pmid:9667942 fatcat:jmjw5sixcfdvle3t3i3brax6b4

Bioinorganic chemistry

Jeremy M Berg, Stephen J Lippard
2004 Current Opinion in Chemical Biology  
We thank them for their contributions. Even with all this help, the book would never have seen the light of day had it not been for the dedication and hard work of Debbie Wuttke.  ...  vii viii Acknowledgments The idea of preparing a bioinorganic chemistry textbook was conceived by one of us (IB) at a "Metals in Biology" Gordon Conference in January, 1986.  ...  P. k_ 1 Approximated as the reciprocal ratio between on-and off-rate constants relevant to the solute-protein complex, lIK m = k]/k_] may be taken as a lower limit of the affinity of the protein for the  ... 
doi:10.1016/j.cbpa.2004.02.014 fatcat:3qfnrjnzmncs5gepeyksdzgbti
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