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Biologistics—Diffusion coefficients for complete proteome of Escherichia coli

Tomasz Kalwarczyk, Marcin Tabaka, Robert Holyst
2012 Computer applications in the biosciences : CABIOS  
contain the complete information about the diffusion coefficients of proteins in a given cell type.  ...  We exemplify the method with the database of in vivo DC for all proteins (4,302 records) from the proteome of K12 strain of E. coli, together with examples of DC of amino acids, sugars, RNA and DNA.  ...  Marcin Fialkowski for inspiring discussions.  ... 
doi:10.1093/bioinformatics/bts537 pmid:22942021 pmcid:PMC3496334 fatcat:f7zl5oyx4zcfndq2miqnouknyy

Mathematical modeling of gene expression: a guide for the perplexed biologist

Ahmet Ay, David N. Arnosti
2011 Critical reviews in biochemistry and molecular biology  
for quantitative understanding of biological systems.  ...  For those interested in beginning a transcriptional mathematical modeling project, we provide here an overview of major types of models and their applications to transcriptional networks.  ...  Declaration of interest The authors declare to have no conflict of interest. The authors alone are responsible for the content and the writing of the manuscript.  ... 
doi:10.3109/10409238.2011.556597 pmid:21417596 pmcid:PMC3086598 fatcat:uei7p4jtbnfoxfpm67va4ucwrq

Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

Juan Javier Díaz-Mejía, Mohan Babu, Andrew Emili
2009 FEMS Microbiology Reviews  
In this review, we summarize the state of the art of computational and proteomic approaches for determining the components of the E. coli cell-envelope proteome, as well as exploring the physical and functional  ...  Strikingly, however, only half of the c. 1200 putative cell-envelope-related proteins of E. coli currently have experimentally attributed functions, indicating an opportunity for discovery.  ...  Acknowledgements The authors wish to thank Sadhna Phanse, and the anonymous reviewers for their motivating comments during the preparation of this manuscript.  ... 
doi:10.1111/j.1574-6976.2008.00141.x pmid:19054114 pmcid:PMC2704936 fatcat:mohn3yvjangdzest5i7z3f2dgm

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

Markus W. Covert, Iman Famili, Bernhard O. Palsson
2003 Biotechnology and Bioengineering  
This review considers constraints in terms of environmental, physicochemical, and self-imposed regulatory and evolutionary constraints with the purpose of refining current constraintbased models of cell  ...  Cells must abide by a number of constraints. The environmental constraints of cellular behavior and physicochemical limitations affect cellular processes.  ...  The authors thank Markus Herrgard and Jason Papin for helpful discussions and reviews.  ... 
doi:10.1002/bit.10849 pmid:14708117 fatcat:zhsoh3jbonaivbdzwv7euujvke

Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein–protein interaction networks?

Santiago Schnell, Santo Fortunato, Sourav Roy
2007 Proteomics  
In this paper, we investigate the role of protein disorder in the network topology. We find that the disorder of a protein (or of its neighbors) is independent of its number of PPIs.  ...  This result suggests that protein disorder does not play a role in the scale-free architecture of protein networks.  ...  We started downloading the PPI networks for Homo sapiens (human), S. cerevisiae (yeast), Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Escherichia coli (bacterium) from the Biomolecular  ... 
doi:10.1002/pmic.200600455 pmid:17285562 fatcat:ezeofyhi7negpdebvp7hmuxrhq

Isolation and purification ofThermus thermophilusHpaB by a crystallization approach

Tewfik Soulimane, Sarah R. O'Kane, Olga Kolaj
2010 Acta Crystallographica. Section F : Structural Biology and Crystallization Communications  
The oxygenase HpaB is a component of the 4-hydroxyphenylacetate 3-monooxygenase enzyme that is responsible for the hydroxylation of 4-hydroxyphenylacetate.  ...  While isolating integral membrane respiratory complexes from Thermus thermophilus, microcrystals of HpaB were formed. Further purification of the enzyme was achieved by repetitive crystallization.  ...  Based on these observations, two groups, with the Acinetobacter baumannii and Escherichia coli enzymes as representatives, can be identified.  ... 
doi:10.1107/s1744309110003714 pmid:20208179 pmcid:PMC2833055 fatcat:rdegp6dz7zcglbyjknyft7b2ku

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Elijah Roberts, Andrew Magis, Julio O. Ortiz, Wolfgang Baumeister, Zaida Luthey-Schulten, Peter Csermely
2011 PLoS Computational Biology  
We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions.  ...  Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due  ...  Acknowledgments The authors would like to acknowledge John Stone for helpful discussions on implementation of the code on the GPU. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002010 pmid:21423716 pmcid:PMC3053318 fatcat:zyiwxi4vlbdolefsgrvormgr2m

Heparin-Binding Protein: A Novel Biomarker Linking Four Different Cardiovascular Diseases

Yufeng Cai, Xueyan Zhang, Jie Shen, Boyue Jiang, Dehua Hu, Mingyi Zhao
2020 Cardiology Research and Practice  
Clustering coefficients were calculated using Cytoscape, and MCODE was used for subnet analysis.  ...  Moreover, a large number of important HBPs were identified that may be significant for the treatment of these diseases.  ...  : lists of clustering coefficients of Ec_hepint, Ec_not hepint, and Ec_hepint_random.  ... 
doi:10.1155/2020/9575373 pmid:32612856 pmcid:PMC7312699 fatcat:jmjg5g446fbkbkss3r5uu2qkua

Systematic functional analysis of the yeast genome

S Oliver
1998 Trends in Biotechnology  
The genome sequence of the yeast Saccharomyces cerevisiae has provided the first complete inventory of the working parts of a eukaryotic cell.  ...  Systematic and comprehensive approaches to the elucidation of yeast gene function are discussed and the prospects for the functional genomics of eukaryotic organisms evaluated.  ...  FB is grateful to Pfizer Central Research for the provision of a postgraduate research studentship.  ... 
doi:10.1016/s0167-7799(98)01214-1 pmid:9744112 fatcat:bngyipmjprfmhclvt65d5z466e

Does cell biology need physicists?

Charles Wolgemuth
2011 Physics  
Allured by the chic perception and higher funding levels of disease-oriented research, many physicists have migrated to cell biology.  ...  Moraru for useful discussions.  ...  Motivated by their work, Howard Berg was one of the pioneers of quantitative biophysical investigations of the swimming of bacteria and showed that Escherichia coli swims by a series of runs and tumbles  ... 
doi:10.1103/physics.4.4 fatcat:xqcsxe67mnaonlpw73uyoy7d64

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy

Michael Volpers, Nico J. Claassens, Elad Noor, John van der Oost, Willem M. de Vos, Servé W. M. Kengen, Vitor A. P. Martins dos Santos, Ivan A. Berg
2016 PLoS ONE  
We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force).  ...  photosystems and the high ATP maintenance of E. coli.  ...  Major advances in synthetic biology start to allow engineering of complex features related to autotrophy into heterotrophic chassis microorganisms, such as Escherichia coli.  ... 
doi:10.1371/journal.pone.0157851 pmid:27336167 pmcid:PMC4919048 fatcat:cvyhpvaw3fcijlp65233xrbsna

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

C. G. de Oliveira Dal'Molin, L.-E. Quek, R. W. Palfreyman, S. M. Brumbley, L. K. Nielsen
2009 Plant Physiology  
AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism.  ...  AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association  ...  ACKNOWLEDGMENTS We thank Simon Boyes for complementing data curation analysis in AraGEM. We also acknowledge our partners, BSES Ltd. and Metabolix, Inc.  ... 
doi:10.1104/pp.109.148817 pmid:20044452 pmcid:PMC2815881 fatcat:nz3nso2h2rddnnqdlh4y6b6usi

The Impact of Mistranslation on Phenotypic Variability and Fitness

Laasya Samhita, Parth K Raval, Godwin Stephenson, Shashi Thutupalli, Deepa Agashe
2021 Evolution  
For instance, translation errors result in about 10% of cellular proteins carrying altered sequences.  ...  Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations.  ...  ACKNOWLEDGMENTS We thank Vidyanand Nanjundiah and members of the Agashe lab for discussion and critical comments on the manuscript, and Debshankar Banerjee for the MATLAB code used for analysing the single  ... 
doi:10.1111/evo.14179 pmid:33491193 fatcat:63l6ddonbnb7znfpgxxd2pytpa

Biomicrofluidics: Recent trends and future challenges

Tamal Das, Suman Chakraborty
2009 Sadhana (Bangalore)  
Particular emphasis is given on the microfluidics-based handling of DNA, cells, and proteins, as well as fundamental microfluidic considerations for design of biomedical microdevices.  ...  Biomicrofluidics is an active area of research at present, exploring the synergy of microfluidics with cellular and molecular biology, biotechnology, and biomedical engineering.  ...  (Baeumner et al 2001) , Dengue virus (Zaytseva et al 2004) and Escherichia coli (Baeumner et al 2003) .  ... 
doi:10.1007/s12046-009-0035-8 fatcat:7nbvjoc45bfovk7fwommwyxs7a

The Functional Network of the Arabidopsis Plastoglobule Proteome Based on Quantitative Proteomics and Genome-Wide Coexpression Analysis

P. K. Lundquist, A. Poliakov, N. H. Bhuiyan, B. Zybailov, Q. Sun, K. J. van Wijk
2012 Plant Physiology  
An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies.  ...  The PG proteome from Arabidopsis (Arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated PGs and quantitative comparison with the proteomes of unfractionated leaves, thylakoids  ...  ACKNOWLEDGMENTS We thank Carole Daugherty (Cornell Center for Material Research) for critical assistance with the SEM analysis of PG preparations, Richard Medville of Electron Microscopy Sciences for the  ... 
doi:10.1104/pp.111.193144 pmid:22274653 pmcid:PMC3291262 fatcat:hdkvtstvzjf4xoedwzk77y2gbm
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