scholarly journals A Novel Approach to Predict Core Residues on Cancer-Related DNA-Binding Domains

2016 ◽  
Vol 15s2 ◽  
pp. CIN.S39366 ◽  
Author(s):  
Ka-Chun Wong
Keyword(s):  
Dna Binding ◽  
Structural Data ◽  
Computational Method ◽  
Prediction Algorithm ◽  
Dna Interactions ◽  
Dna Binding Domains ◽  
Cancer Pathways ◽  
The Core ◽  
Binding Domains ◽  
Protein Dna Interactions

Protein–DNA interactions are involved in different cancer pathways. In particular, the DNA-binding domains of proteins can determine where and how gene regulatory regions are bound in different cell lines at different stages. Therefore, it is essential to develop a method to predict and locate the core residues on cancer-related DNA-binding domains. In this study, we propose a computational method to predict and locate core residues on DNA-binding domains. In particular, we have selected the cancer-related DNA-binding domains for in-depth studies, namely, winged Helix Turn Helix family, homeodomain family, and basic Helix-Loop-Helix family. The results demonstrate that the proposed method can predict the core residues involved in protein–DNA interactions, as verified by the existing structural data. Given its good performance, various aspects of the method are discussed and explored: for instance, different uses of prediction algorithm, different protein domains, and hotspot threshold setting.

scholarly journals The Ig fold of the core binding factor α Runt domain is a member of a family of structurally and functionally related Ig-fold DNA-binding domains

Structure ◽  
1999 ◽  
Vol 7 (10) ◽  
pp. 1247-1256 ◽  
Author(s):  
Marcelo J Berardi ◽  
Chaohong Sun ◽  
Michael Zehr ◽  
Frits Abildgaard ◽  
Jeff Peng ◽  
...  
Keyword(s):  
Dna Binding ◽  
Runt Domain ◽  
Core Binding Factor ◽  
Dna Binding Domains ◽  
The Core ◽  
Binding Domains ◽  
Binding Factor ◽  
Factor Α

scholarly journals On exploring effects of coevolving residues on DNA binding specificity of transcription factors

2021 ◽  
Author(s):  
Yizhao Luan ◽  
Zhi Xie
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Specificity ◽  
Binding Activity ◽  
Dna Interactions ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Activity ◽  
Dna Binding Specificity ◽  
The Stability

Transcription factors (TFs) regulate gene expression by specifically binding to DNA targets. Many factors have been revealed to influence TF-DNA binding specificity. Coevolution of residues in proteins occurs due to a common evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically analyzed TF-DNA interactions from high-throughput experiments for seven TF families, including Homeobox, HLH, bZIP_1, Ets, HMG_box, zf-C4 and Zn_clus TFs. Based on TF-DNA interactions, we detected TF subclass determining sites (TSDSs) defining the heterogeneity of DNA binding preference for each TF family. We showed that the TSDSs were more likely to be coevolving with TSDSs than with non-TSDSs, particularly for Homeobox, HLH, Ets, bZIP_1 and HMG_box TF families. 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.

scholarly journals Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1

2014 ◽  
Vol 289 (31) ◽  
pp. 21605-21616 ◽  
Author(s):  
Shuo Wang ◽  
Miles H. Linde ◽  
Manoj Munde ◽  
Victor D. Carvalho ◽  
W. David Wilson ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Ets Family ◽  
Site Recognition

scholarly journals Protein Kinase A Signaling Pathway Regulates Transcriptional Activity of SAF-1 by Unmasking Its DNA-binding Domains

2003 ◽  
Vol 278 (25) ◽  
pp. 22586-22595 ◽  
Author(s):  
Alpana Ray ◽  
Papiya Ray ◽  
Nicole Guthrie ◽  
Arvind Shakya ◽  
Deepak Kumar ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Dna Binding ◽  
Protein Kinase A ◽  
Signaling Pathway ◽  
Transcriptional Activity ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Kinase A

scholarly journals Role of Papillomavirus E1 Initiator Dimerization in DNA Replication

2005 ◽  
Vol 79 (13) ◽  
pp. 8661-8664 ◽  
Author(s):  
Stephen Schuck ◽  
Arne Stenlund
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Severe Effect ◽  
Origin Of Dna Replication ◽  
Initiation Of Dna Replication

ABSTRACT Viral initiator proteins are polypeptides that form oligomeric complexes on the origin of DNA replication (ori). These complexes carry out a multitude of functions related to initiation of DNA replication, and although many of these functions have been characterized biochemically, little is understood about how the complexes are assembled. Here we demonstrate that loss of one particular interaction, the dimerization between E1 DNA binding domains, has a severe effect on DNA replication in vivo but has surprisingly modest effects on most individual biochemical activities in vitro. We conclude that the dimer interaction is primarily required for initial recognition of ori.

scholarly journals Cdc13 N-Terminal Dimerization, DNA Binding, and Telomere Length Regulation

2010 ◽  
Vol 30 (22) ◽  
pp. 5325-5334 ◽  
Author(s):  
Meghan T. Mitchell ◽  
Jasmine S. Smith ◽  
Mark Mason ◽  
Sandy Harper ◽  
David W. Speicher ◽  
...  
Keyword(s):  
Dna Binding ◽  
Telomere Length ◽  
Functional Characterization ◽  
Point Mutations ◽  
Telomeric Dna ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Length Regulation ◽  
Telomere Length Regulation

ABSTRACT The essential yeast protein Cdc13 facilitates chromosome end replication by recruiting telomerase to telomeres, and together with its interacting partners Stn1 and Ten1, it protects chromosome ends from nucleolytic attack, thus contributing to genome integrity. Although Cdc13 has been studied extensively, the precise role of its N-terminal domain (Cdc13N) in telomere length regulation remains unclear. Here we present a structural, biochemical, and functional characterization of Cdc13N. The structure reveals that this domain comprises an oligonucleotide/oligosaccharide binding (OB) fold and is involved in Cdc13 dimerization. Biochemical data show that Cdc13N weakly binds long, single-stranded, telomeric DNA in a fashion that is directly dependent on domain oligomerization. When introduced into full-length Cdc13 in vivo, point mutations that prevented Cdc13N dimerization or DNA binding caused telomere shortening or lengthening, respectively. The multiple DNA binding domains and dimeric nature of Cdc13 offer unique insights into how it coordinates the recruitment and regulation of telomerase access to the telomeres.

Conformational changes in the DNA-binding domains of the ecdysteroid receptor during the formation of a complex with the hsp27 response element

2012 ◽  
Vol 30 (4) ◽  
pp. 379-393 ◽  
Author(s):  
Szymon Pakuła ◽  
Marek Orłowski ◽  
Grzegorz Rymarczyk ◽  
Tomasz Krusiński ◽  
Michał Jakób ◽  
...  
Keyword(s):  
Dna Binding ◽  
Conformational Changes ◽  
Response Element ◽  
Ecdysteroid Receptor ◽  
Dna Binding Domains ◽  
Binding Domains
Sign in / Sign up

Export Citation Format

Share Document