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Protein post-translational modifications: In silico prediction tools and molecular modeling

Martina Audagnotto, Matteo Dal Peraro
2017 Computational and Structural Biotechnology Journal  
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics.  ...  of post-translational modified proteins.  ...  PTMs cross-talk The hypothesis of a correlation between PTMs within the same protein (PTMs cross-talk) [285] has emerged in the proteomic field in recent years.  ... 
doi:10.1016/j.csbj.2017.03.004 pmid:28458782 pmcid:PMC5397102 fatcat:iuibks5owba4tjnscxfvm2dyi4

Co-occurring protein phosphorylation are functionally associated

Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li, Predrag Radivojac
2017 PLoS Computational Biology  
Post-translational modifications (PTMs) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions.  ...  Co-occurring phosphorylation occurs significantly more frequently than randomly expected and include many known examples of cross-talk or functional connections.  ...  Torsten Juelich (Peking University, China) for critical reading and editing the draft version of this manuscript. Visualization: YL XZ. Writing -original draft: TL YL XZ.  ... 
doi:10.1371/journal.pcbi.1005502 pmid:28459814 pmcid:PMC5432191 fatcat:ovcvlmfjmjhknjupa35f22o34i

Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones

Gabrielle Stetz, Amanda Tse, Gennady M. Verkhivker
2018 Scientific Reports  
Dissecting structure-encoded determinants of allosteric cross-talk between post-translational modification sites in the Hsp90 chaperones. Sci Rep 8, 6899, https://doi.  ...  Post-translational modifications (PTMs) represent an important regulatory instrument that modulates structure, dynamics and function of proteins.  ...  Author Contributions G.V. designed and supervised this study. G.S. and A.T. performed simulations and analyzed the results. G.V. analyzed and interpreted the data and wrote the manuscript.  ... 
doi:10.1038/s41598-018-25329-4 pmid:29720613 pmcid:PMC5932063 fatcat:myzd2ceo4vdtxdfi62iua7zili

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

2018 Briefings in Bioinformatics  
Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins.  ...  We cover a variety of important aspects that are crucial for the development of successful predictors, including operating algorithms, sequence and structural features, feature selection, model performance  ...  Introduction Post-translational modifications (PTMs) occurring at the lysine (K) residues of proteins, such as acetylation, glutarylation, glycation, malonylation, methylation, succinylation, sumoylation  ... 
doi:10.1093/bib/bby089 pmid:30285084 pmcid:PMC6954452 fatcat:ipqhpnlhufegnodxthnwl75t4y

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

S. A. Shabalina, N. A. Spiridonov, A. Kashina
2013 Nucleic Acids Research  
post-translational modifications of nascent polypeptides.  ...  Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and  ...  ACKNOWLEDGEMENTS The authors thank Fangliang Zhang and Aleksey Ogurtsov for providing the data for Figures 2 and 5 , Pavel Baranov and Olga Matveeva for stimulating discus-  ... 
doi:10.1093/nar/gks1205 pmid:23293005 pmcid:PMC3575835 fatcat:d36krcvzbbfavim2bk4sqhj5sy

A Census and Categorization Method of Epitranscriptomic Marks

Julia Mathlin, Loredana Le Le Pera, Teresa Colombo
2020 International Journal of Molecular Sciences  
layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs).  ...  Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications ("stages") until reaching the  ...  cross-talks) and allows to overlay variable levels of details, such as organisms, synthetic pathways, and interacting partners.  ... 
doi:10.3390/ijms21134684 pmid:32630140 pmcid:PMC7370119 fatcat:rsy2wwdwcbavjlzbdbfxptxk5u

Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities

Sagnik Sen, Ashmita Dey, Sanghamitra Bandhyopadhyay, Vladimir N Uversky, Ujjwal Maulik
2021 Briefings in Bioinformatics  
However, studies on the sequences and structure space throughout the evolutionary time frame of viral proteins are limited.  ...  Based on the host cell proteins, the diseases are divided in two distinct classes: (i) proteins, directly associated with the set of diseases while showing similar activities, and (ii) cytokine storm-mediated  ...  Most importantly, we would like to thank the reviewers for their valuable comments and suggestions which helped us improve the quality of the paper.  ... 
doi:10.1093/bib/bbab232 pmid:34143202 fatcat:3b7x626ycjbydmh7o3oavhjsne

Demystifying O-GlcNAcylation: hints from peptide substrates

Jie Shi, Rob Ruijtenbeek, Roland J Pieters
2018 Glycobiology  
O-GlcNAcylation, analogous to phosphorylation, is an essential post-translational modification of proteins at Ser/Thr residues with a single β-N-acetylglucosamine moiety.  ...  This dynamic protein modification regulates many fundamental cellular processes and its deregulation has been linked to chronic diseases such as cancer, diabetes and neurodegenerative disorders.  ...  Introduction O-GlcNAcylation is a ubiquitous post-translational modification (PTM) of serine or threonine residues with a single O-linked β-Nacetylglucosamine (O-GlcNAc) on numerous proteins.  ... 
doi:10.1093/glycob/cwy031 pmid:29635275 fatcat:3pov2oipfbdb3ocssgqthjs6p4

Overview of tRNA Modifications in Chloroplasts

Maxime Fages-Lartaud, Martin Frank Hohmann-Marriott
2022 Microorganisms  
Nucleotide modifications within a minimal set of tRNAs modulate codon–anticodon interactions that are crucial for translation efficiency.  ...  Here, we synthesize all available information concerning tRNA modifications in the chloroplast and assign translation efficiency for each modified anticodon–codon pair.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/microorganisms10020226 pmid:35208681 pmcid:PMC8877259 fatcat:jnnoe7gc6fhjtkg3xclxoqfzwy

Small nucleolar RNAs controlling rRNA processing in Trypanosoma brucei

Vaibhav Chikne, K Shanmugha Rajan, Moran Shalev-Benami, Kathryn Decker, Smadar Cohen-Chalamish, Hava Madmoni, Viplov K Biswas, Sachin Kumar Gupta, Tirza Doniger, Ron Unger, Christian Tschudi, Elisabetta Ullu (+1 others)
2019 Nucleic Acids Research  
Interestingly, the 6 snoRNAs that affect srRNA1 processing guide modifications on rRNA positions that span locations from the protein exit tunnel to the srRNA1, suggesting that these modifications may  ...  Five of these snoRNAs interact with the intervening sequences of rRNA precursor, whereas the others only guide rRNA modifications. The function of the snoRNAs was explored by silencing snoRNAs.  ...  ACKNOWLEDGEMENTS The authors dedicate this study to the memory of Elisabetta Ullu an exceptional creative and inspiring scientist, a leader of our field, and above all a dear friend and generous colleague  ... 
doi:10.1093/nar/gky1287 pmid:30605535 pmcid:PMC6411936 fatcat:2hh4qnaiubbthkl2kos2xyu3eq

Intrinsic Structural Disorder in Cytoskeletal Proteins

Mainak Guharoy, Beata Szabo, Sara Contreras Martos, Simone Kosol, Peter Tompa
2013 Cytoskeleton  
accessory proteins/regions being highly disordered, and are responsible for most of the regulatory (post-translational) input promoting adaptive responses and providing dynamics necessary for each of  ...  Here, we elaborate on the idea that the opposing features of stability and dynamics are also manifest in the dichotomy of the structural status of its components, the core being highly structured and the  ...  The authors declare no conflict of interest.  ... 
doi:10.1002/cm.21118 pmid:23761374 fatcat:h7ved6rcwbb4rkjnfgukuhyuba

The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation

Francesca Chignola, Massimiliano Gaetani, Ana Rebane, Tõnis Org, Luca Mollica, Chiara Zucchelli, Andrea Spitaleri, Valeria Mannella, Pärt Peterson, Giovanna Musco
2009 Nucleic Acids Research  
Here, we present the solution structure of AIRE-PHD1 in complex with H3K4me0 peptide and show that AIRE-PHD1 is a highly specialized non-modified histone H3 tail reader, as post-translational modifications  ...  The observed antagonism by R2 methylation on AIRE-PHD1 binding is unique among the H3K4me0 histone readers and represents the first case of epigenetic negative cross-talk between non-methylated H3K4 and  ...  ACKNOWLEDGEMENTS We thank Marco Bianchi and Davide Gabellini for critical reading of the manuscript. The authors acknowledge Maire Pihlap for technical help.  ... 
doi:10.1093/nar/gkp166 pmid:19293276 pmcid:PMC2685098 fatcat:fecfgy2jgzdmrekx7465kmh7xi

Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

Tugba Kucukkal, Ye Yang, Susan Chapman, Weiguo Cao, Emil Alexov
2014 International Journal of Molecular Sciences  
DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and  ...  expressed proteins.  ...  Author Contributions Tugba Kucukkal and Emil Alexov wrote the in silico Section; Ye Yang and Weiguo Cao wrote the in vitro Section and Susan Chapman wrote the in vivo Section.  ... 
doi:10.3390/ijms15069670 pmid:24886813 pmcid:PMC4100115 fatcat:wvilvvfkmfbz3owuys6qjz4npq

RNA loop–loop interactions as dynamic functional motifs

Christine Brunel, Roland Marquet, Pascale Romby, Chantal Ehresmann
2002 Biochimie  
Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme.  ...  Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.  ...  Acknowledgements We wish to thank all the members of the laboratory who have contributed or/and still contribute to the work described in this review, as well as members of other laboratories who provided  ... 
doi:10.1016/s0300-9084(02)01401-3 pmid:12458085 fatcat:oxns4v2anrgszimvkpri5geecy

From snoRNA to miRNA: Dual function regulatory non-coding RNAs

Michelle S. Scott, Motoharu Ono
2011 Biochimie  
Small nucleolar RNAs (snoRNAs) are an ancient class of small non-coding RNAs present in all eukaryotes and a subset of archaea that carry out a fundamental role in the modification and processing of ribosomal  ...  In parallel, several studies have uncovered extensive similarities between snoRNAs and other types of small non-coding RNAs, and in particular microRNAs.  ...  Acknowledgements The authors wish to thank Professors Angus Lamond and Geoff Barton for insightful discussions.  ... 
doi:10.1016/j.biochi.2011.05.026 pmid:21664409 pmcid:PMC3476530 fatcat:i7quds3yfrhr5khyumtex5de6a
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