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Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example [chapter]

Álvaro Sebastián, Carlos P. Cantalapiedra, Bruno Contreras-Moreira
2012 Lecture Notes in Computer Science  
proteins might bind to the same DNA motif.  ...  This repository can be scanned by means of sequence alignments in order to look for similar DNA-binding proteins, which might in turn recognize similar DNA motifs.  ...  Defining a consensus Homeobox protein-DNA interface Homeobox proteins (and in general homeodomain-like proteins) usually bind to DNA with a conserved architecture.  ... 
doi:10.1007/978-3-642-28062-7_8 fatcat:taow7ed2pvgohg5kmp7gwe534u

Building an automated classification of DNA-binding protein domains

J. V. Ponomarenko, P. E. Bourne, I. N. Shindyalov
2002 Bioinformatics  
Comparison with existing resources on describing structural and functional classifications of DNA-binding proteins was used to validate and improve the approach proposed here.  ...  The approach involves the analysis of 3D-interaction patterns in DNA-protein interfaces, assignment of structural domains interacting with DNA, clustering of domains based on structural similarity and  ...  ACKNOWLEDGMENT This work was supported by the National Partnership for Advanced Computational Infrastructure from the National Science Foundation, and NSF Grants DBI 9808706, DBI 0111710, and NIH NIGMS  ... 
doi:10.1093/bioinformatics/18.suppl_2.s192 pmid:12386003 fatcat:ygrrmwzlh5gwzdy3iwga35uobm

NPIDB: nucleic acid—protein interaction database

Dmitry D. Kirsanov, Olga N. Zanegina, Evgeniy A. Aksianov, Sergei A. Spirin, Anna S. Karyagina, Andrei V. Alexeevski
2012 Nucleic Acids Research  
The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved  ...  water molecules on the DNA-protein interface.  ...  ACKNOWLEDGEMENTS The authors thank Alexey Salnikov for participation in creating the new version of the program CluD, which is used for calculation of hydrophobic interactions between macromolecules, Elena  ... 
doi:10.1093/nar/gks1199 pmid:23193292 pmcid:PMC3531207 fatcat:pxvf4djhcrhppovivekhkok2dm

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata (+4 others)
2017 Protein Science  
surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.  ...  The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures.  ...  After the gmfit refinement, all of the structures that ranked in the top 50 were DNA gyrases or related molecular complexes. The last improvement is about the gmfit comparison.  ... 
doi:10.1002/pro.3273 pmid:28815765 pmcid:PMC5734392 fatcat:7ttn55ucxvcjfjkmivznvmet34

Linkers in the structural biology of protein-protein interactions

Vishnu Priyanka Reddy Chichili, Veerendra Kumar, J. Sivaraman
2013 Protein Science  
The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers.  ...  In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein-protein complexes, and to obtain protein dimers.  ...  Acknowledgements We are grateful to the Academic Research Funding (AcRF), National University of Singapore (NUS), Singapore, for the support of this study.  ... 
doi:10.1002/pro.2206 pmid:23225024 pmcid:PMC3588912 fatcat:2oynsgw75zgulks7p573ggq4au

Towards region-specific propagation of protein functions [article]

Da Chen Emily Koo, Richard Bonneau
2018 bioRxiv   pre-print
Due to the nature of experimental annotation, most protein function prediction methods operate at the protein-level, where functions are assigned to full-length proteins based on overall similarities.  ...  We apply this method to local features obtained from InterPro, UniProtKB and amino acid sequences and show that this method improves both the accuracy and region-specificity of protein function transfer  ...  Structural examples of improved label localization Here we leverage the very large diversity of RNA and DNA binding proteins with known structures to investigate the performance and resolution of our method  ... 
doi:10.1101/275487 fatcat:uteeq6xaqvgkrfoq5yzdox3l3e

Homeodomain Proteins Directly Regulate ATM Kinase Activity

Tanya E. Johnson, Ji-Hoon Lee, Logan R. Myler, Yi Zhou, Trenell J. Mosley, Soo-Hyun Yang, Nadima Uprety, Jonghwan Kim, Tanya T. Paull
2018 Cell Reports  
In Brief Johnson et al. demonstrate that several members of the homeobox transcription factor family bind directly to the ATM protein kinase and to the MRN complex, inhibiting activation of ATM by DNA  ...  These results suggest that homeobox proteins may act as tissuespecific regulators of the DNA damage response.  ...  ACKNOWLEDGMENTS We thank members of the Paull laboratory for helpful suggestions and to Edward Gelmann for initial ideas and reagents. Lac Repressor was a gift from Ilya Finkelstein.  ... 
doi:10.1016/j.celrep.2018.06.089 pmid:30089259 pmcid:PMC6127865 fatcat:aexfbeims5dbpildxzwe6gqwhu

Automatically extracting functionally equivalent proteins from SwissProt

Lisa EM McMillan, Andrew CR Martin
2008 BMC Bioinformatics  
However there has been no resource allowing the easy, automatic extraction of groups of FEPs -for example, all instances of protein C.  ...  The method builds a candidate list of homologues and filters out functionally diverged proteins on the basis of functional annotations using a simple text mining approach.  ...  Acknowledgements We thank Rolf Apweiler and Michele Magrane for useful discussions regarding UniProtKB/SwissProt annotations and David Jones for valuable discussions about the manuscript.  ... 
doi:10.1186/1471-2105-9-418 pmid:18838004 pmcid:PMC2576269 fatcat:cxrucluiszhjrpbqymr4tumdxm

On exploring effects of coevolving residues on DNA binding specificity of transcription factors [article]

Yizhao Luan, Zhi Xie
2021 bioRxiv   pre-print
Mutation of the highly coevolving residues could significantly reduce the stability of TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity.  ...  Overall, our study gave evidence of the functional importance of coevolved residues in refining transcriptional regulation and provided clues to the application of engineered DNA-binding domains and protein  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China (31900477 to YZ.L.), and China Postdoctoral Science Foundation (2018M633217 to YZ.L.).  ... 
doi:10.1101/2021.05.20.445059 fatcat:dsda6676ibdedl555x3xlvngo4

Protein classification using ontology classification

K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, R. Stevens
2006 Bioinformatics  
Motivation: The classification of proteins expressed by an organism is an important step in understanding the molecular biology of that organism.  ...  Results: We capture human understanding of how to recognise members of the protein phosphatases family by domain architecture as an ontology.  ...  Sequencing of Aspergillus fumigatus was funded by the National Institute of Allergy and Infectious Disease U01 AI 48830 to David Denning and William Nierman, the Wellcome Trust, and Fondo de Investicagiones  ... 
doi:10.1093/bioinformatics/btl208 pmid:16873517 fatcat:dcmi2leprzgexpsjzlxho3mvdi

Structural aspects of protein-DNA recognition

P S Freemont, A N Lane, M R Sanderson
1991 Biochemical Journal  
The homeobox genes involved in embryonic segmentation in for example Drosophila contain a 60-residue motif that codes for a DNA-binding protein called the homeodomain protein. protein have been initiated  ...  However, a three-dimensional comparison of all helix-turn-helix motifs has shown that these latter proteins are less similar to A cro repressor than those proteins which are involved in DNA-binding and  ... 
doi:10.1042/bj2780001 pmid:1883321 pmcid:PMC1151442 fatcat:xomj4u62ovdgrgp3youww6wfke

Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins

M. Quadir Siddiqui, Maulik D. Badmalia, Trushar R. Patel
2021 International Journal of Molecular Sciences  
Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity.  ...  Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3.  ...  Protein SVM Score * Prediction Job Number on Webserver Zyxin 1.2919473 DNA binding protein 1710 LimD1 0.90588128 DNA binding protein 4069 Ajuba 1.4081202 DNA binding protein 7780 LPP 0.11482763 DNA binding  ... 
doi:10.3390/ijms22052647 pmid:33808029 pmcid:PMC7961639 fatcat:w453oyzxpnhz3pftt7prjckdl4

Contextual Specificity in Peptide-Mediated Protein Interactions

Amelie Stein, Patrick Aloy, Lennart Randau
2008 PLoS ONE  
We found that, on average, the context is responsible for roughly 20% of the binding and plays a crucial role in determining interaction specificity, by either improving the affinity with the native partner  ...  We also studied and quantified the topological and energetic variability of interaction interfaces, finding a much higher heterogeneity in the context residues than in the consensus binding motifs.  ...  Nuclear receptors have 4 interaction interfaces: a ligand-binding pocket that holds lipophilic compounds (e.g., hormones like oestrogen), the cofactor binding groove, a dimerization interface, and a DNA-binding  ... 
doi:10.1371/journal.pone.0002524 pmid:18596940 pmcid:PMC2438476 fatcat:5ccikd2ztfg3vhssafct2f3nui

Master Proteins Dictate Retinal Differentiation Timetable

Liza Gross
2006 PLoS Biology  
The genome sequence of the single-celled ciliate Tetrahymena thermophila sheds light on early eukaryotic evolution.  ...  M, et al. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.  ...  DOI: 10.1371/ journal.pbio.0040298 DOI: 10.1371/journal.pbio.0040314.g001 The long, sticky fi laments covering E. coli bacteria uncoil under force, apparently improving the binding of the terminal adhesive  ... 
doi:10.1371/journal.pbio.0040293 pmid:20076631 pmcid:PMC1540711 fatcat:qyuwizmskrarxap26mpnrurohu

Bioinformatic Analysis of Structure and Function of Lim Domains of Zyxin Family of Proteins [article]

Mohammad Quadir Siddiqui, Maulik D. Badmalia, Trushar R. Patel
2020 bioRxiv   pre-print
Molecular modeling and structural analysis demonstrate that Lim domains of the members of the Zyxin family proteins share similarities with transcriptional regulators, suggesting they could interact with  ...  Our comprehensive analysis of the Zyxin family proteins indicates that the Lim domains function in a variety of ways and could be implicated in rational protein engineering and might lead as a better therapeutic  ...  4069 Ajuba 1.4081202 DNA binding protein 7780 LPP 0.11482763 DNA binding protein 1668 WTIP 1.7520286 DNA binding protein 1032 FBLIM1 0.39872591 DNA binding protein 1215 *= Calculated for full length (  ... 
doi:10.1101/2020.07.14.202572 fatcat:xodtiyicnbepfp3wmi4ytrn66i
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