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The RNA-Protein World

S. Altman
2013 RNA: A publication of the RNA Society  
world should be labeled as the RNA-Protein World.  ...  Following the naming of the RNA World for the hypothetical biochemical world during very early life forms, the current world was named the Protein World.  ...  the view that our current world is not the Protein World but, rather, the RNA-Protein World.  ... 
doi:10.1261/rna.038687.113 pmid:23592800 pmcid:PMC3677274 fatcat:4uu4qofrhveltobjxel5oggafi

The world of protein acetylation

Adrian Drazic, Line M. Myklebust, Rasmus Ree, Thomas Arnesen
2016 Biochimica et Biophysica Acta - Proteins and Proteomics  
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level.  ...  The acetyl group, donated by the metabolite acetylcoenzyme A, can be co-or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues  ...  Acknowledgements The authors gratefully acknowledge support by the Bergen Research Foundation BFS to T.A. and L.M.M., the Research Council of Norway (grants 230865 and 249843) to T.A., the Norwegian Cancer  ... 
doi:10.1016/j.bbapap.2016.06.007 pmid:27296530 fatcat:43xeqi2knbemzhkveuxzkoa2mm

The Porous Borders of the Protein World

Matthew H.J. Cordes, Katie L. Stewart
2012 Structure  
Fold switching may play a role in the evolution of new protein folds and functions.  ...  ., in this issue of Structure, use protein design to illustrate that the same drastic change in a protein fold can occur via multiple different mutational pathways.  ...  In the protein world, one equivalent of a march might be a set of similar sequences, or a region of sequence space, encoding two different detectable folds and/or two detectable associated functions.  ... 
doi:10.1016/j.str.2012.01.015 pmid:22325767 fatcat:hr3ts45fgjajlgh7dzqixlvp3e

The alleviation of the world protein shortage

A. A. Woodham
1969 Proceedings of the Nutrition Society  
The alleviation of the world protein shortage By A. A.  ...  ever-increasing world population.  ... 
doi:10.1079/pns19690015 pmid:5815041 fatcat:7kxoez5f35eobdfa4btki2yuuq

When protein engineering confronts the tRNA world

P. Schimmel, D. Soll
1997 Proceedings of the National Academy of Sciences of the United States of America  
The tRNA World The tRNA world encompasses a large area of biology and chemistry (2).  ...  A long-outstanding goal of protein engineering has run up against the tRNA world, a situation that, in turn, makes the achievement of that goal a formidable challenge.  ...  when protein engineering confronts the tRNA world.  ... 
doi:10.1073/pnas.94.19.10007 pmid:9294151 pmcid:PMC33764 fatcat:ios4dcg2dnhzpeoocsj4uo3iui

DING Proteins Extend to the Extremophilic World

Elena Porzio, Maria Rosaria Faraone Mennella, Giuseppe Manco
2021 International Journal of Molecular Sciences  
The DING proteins are ubiquitous in the three domains of life, from mesophiles to thermo- and hyperthermophiles.  ...  This review is an update of the most recent findings on old and new DING proteins.  ...  E.P. dedicates this review to the author M.R.F.M., who first discovered a DING protein from Archaea; E.P. wants to celebrate her laudable person and academic career.  ... 
doi:10.3390/ijms22042035 pmid:33670786 pmcid:PMC7922408 fatcat:rtbekcdkjbcstg2qmtmzhsirde

The prion protein and New World primate phylogeny

Igor Schneider, Horacio Schneider, Maria Paula Schneider, Artur Silva
2004 Genetics and Molecular Biology  
Variations in the prion protein gene were observed among 16 genera of New World primates (Platyrrhini), and resulted in amino acid substitutions when compared with the human sequence.  ...  The PrP C prion protein contains 250 amino acids with some variation among species and is expressed in several cell types.  ...  In the present paper, we increase the number of taxa of New World primates, including members of all 16 extant genera in an attempt to assess the usefulness of prion protein gene for resolving phylogenetic  ... 
doi:10.1590/s1415-47572004000400007 fatcat:pnwyzdpubvfffdsdj7hnzzacvu

A bridge between the RNA and protein worlds?

Robert C Bergstrom, Lynn D Mayfield, David R Corey
2001 Chemistry and Biology  
RNA can catalyze diverse chemical reactions, leading to the hypothesis that an RNA world existed early in evolution.  ...  Today, however, catalysis by naturally occurring RNAs is rare and most chemical transformations within cells require proteins.  ...  Acknowledgements This work was supported by Grants from the Robert A. Welch Foundation (I-1244) and the National Institutes of Health GM 60642.  ... 
doi:10.1016/s1074-5521(01)00004-7 pmid:11251293 fatcat:f6z7gphcvjg53hs3oyfcyfxcxa

Proteins in Wonderland: The Magical World of Pressure

Kazuyuki Akasaka, Akihiro Maeno
2021 Biology  
Provided that the solution conditions (temperature, pH, etc.) remain largely the same, the idea provides a general method for choosing N, U, or F of a protein, to a great extent at will, assisted by the  ...  Admitting the "Native", "Unfolded" and "Fibril" states as the three basic generic states of proteins in nature, each of which is characterized with its partial molar volume, here we predict that the interconversion  ...  The funder had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/biology11010006 pmid:35053003 pmcid:PMC8772990 fatcat:z5p7fufqrzbd7jvwumjdzalmei

Protein crystallization analysis on the World Community Grid

Christian A. Cumbaa, Igor Jurisica
2010 Journal of Structural and Functional Genomics  
Image analysis for this system is performed by the Help Conquer Cancer (HCC) project on the World Community Grid.  ...  Keywords Image analysis Á High-throughput protein crystallization Abbreviations HWI Hauptman-woodward medical research institute WCG World community grid HCC Help conquer cancer GLCM Grey-level co-occurrence  ...  Acknowledgments We wish to thank the many members of the World Community Grid, who donated their computing resources to the Help Conquer Cancer project.  ... 
doi:10.1007/s10969-009-9076-9 pmid:20072819 pmcid:PMC2857471 fatcat:xkccvwgjgrcwdhpl2q2v7rtnue

High Pressure NMR Expands the Protein Structure World
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Kazuyuki AKASAKA
2002 Seibutsu Butsuri  
. , , pH Fig.2 A simplified picture showing how the partial molar volume of a protein may change with pressure.  ...  , A protein in solution is a thermodynamic entity, consisting of ensemble of conformers ranging from the lowest-energy folded conformer to the highest-energy unfolded conformer.  ... 
doi:10.2142/biophys.42.206 fatcat:y56vp2o4urevdb3zcorb2qrzl4

Why aren't the small worlds of protein contact networks smaller [article]

Susan Khor
2011 arXiv   pre-print
Hence there can be explanations, other than the excluded volume argument, beneath the topological limits of protein contact networks.  ...  Results from the experiments also led to observations which parallel an existing view that neither short-range nor long-range interactions dominate the protein folding process.  ...  The need for rapid communication between amino acid residues to facilitate interaction cooperativity crucial for protein folding is frequently cited as the reason for the small-world feature of PRNs (  ... 
arXiv:1101.2229v2 fatcat:aaiakk73yzakjmbbhc6clihnf4

Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains

Nikolay M. Borisov, Nick I. Markevich, Jan B. Hoek, Boris N. Kholodenko
2006 Biosystems (Amsterdam. Print)  
Membrane receptors and proteins involved in signal transduction display numerous binding domains and operate as molecular scaffolds generating a variety of parallel reactions and protein complexes.  ...  We specify the conditions when the temporal dynamics of micro-states can be exactly or approximately expressed in terms of the product of the relative concentrations of separate domains.  ...  ACKNOWLEDGEMENTS This work was supported by the Grants GM59570 and AA08714 from the National Institute of Health.  ... 
doi:10.1016/j.biosystems.2005.03.006 pmid:16242235 pmcid:PMC1477537 fatcat:e63gt2ijl5dxxopawsxdsjwjla

Combining Bioinformatics and Biophysics to Understand Protein-Protein and Protein-Ligand Interactions

Barry Honig
2002 The Scientific World Journal  
combined use, with specific application to understanding the principles of protein-protein and protein-ligand interactions.  ...  The increasing numbers of proteins whose three-dimensional structures have been determined will have major impact on the ability to exploit genomic data.  ...  This work was supported by the NIH GM30518, NSF grants MCB-9808902 and DBI-9904841.  ... 
doi:10.1100/tsw.2002.22 pmid:29973796 pmcid:PMC6009729 fatcat:adohpto36jakbiywg7olx2eqxu

[GADV]-Protein World Hypothesis on the Origin of Life [chapter]

Kenji Ikehara
2012 Cellular Origin, Life in Extreme Habitats and Astrobiology  
In contrast, I have proposed a more reasonable [GADV]-protein world hypothesis or GADV hypothesis, suggesting that life originated from the protein world, which was formed by pseudo-replication of [GADV  ...  To this end, I have proposed the [GADV]-protein world hypothesis, or the GADV hypothesis in short, for the origin of life (Ikehara 2002; Ikehara 2005; Ikehara 2009; Ikehara 2012).  ...  [GADV]-Protein World Hypothesis  ... 
doi:10.1007/978-94-007-2941-4_6 fatcat:gaxm5h6wsbgkxhmsu2iqxmw57e
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