Detection of the Local Structural Changes in the Dimer Interface ofBamHI Initiated by DNA Binding and Dissociation Using a Solvatochromic Fluorophore

2006 ◽  
Vol 110 (42) ◽  
pp. 21311-21318 ◽  
Author(s):  
Koji Nakayama ◽  
Masayuki Endo ◽  
Mamoru Fujitsuka ◽  
Tetsuro Majima
Keyword(s):  
Dna Binding ◽  
Structural Changes ◽  
Dimer Interface

Repressor Activity of SqrR, a Master Regulator of Persulfide-Responsive Genes, Is Regulated by Heme Coordination

2020 ◽  
Author(s):  
Takayuki Shimizu ◽  
Yuuki Hayashi ◽  
Munehito Arai ◽  
Shawn E McGlynn ◽  
Tatsuru Masuda ◽  
...  
Keyword(s):  
Dna Binding ◽  
Transcriptional Repression ◽  
Structural Changes ◽  
Gene Promoter ◽  
Binding Activity ◽  
Heme Binding ◽  
Master Regulator ◽  
Incremental Change ◽  
Dna Binding Activity

Abstract Reactive sulfur species (RSS) are involved in bioactive regulation via persulfidation of proteins. However, how cells regulate RSS-based signaling and RSS metabolism is poorly understood, despite the importance of universal regulation systems in biology. We previously showed that the persulfide-responsive transcriptional factor SqrR acts as a master regulator of sulfide-dependent photosynthesis in proteobacteria. Here, we demonstrated that SqrR also binds heme at a near one-to-one ratio with a binding constant similar to other heme-binding proteins. Heme does not change the DNA-binding pattern of SqrR to the target gene promoter region; however, DNA-binding affinity of SqrR is reduced by the binding of heme, altering its regulatory activity. Circular dichroism spectroscopy clearly showed secondary structural changes in SqrR by the heme binding. Incremental change in the intracellular heme concentration is associated with small, but significant reduction in the transcriptional repression by SqrR. Overall, these results indicate that SqrR has an ability to bind heme to modulate its DNA-binding activity, which may be important for the precise regulation of RSS metabolism in vivo.

scholarly journals Conformational Changes in the Capsid of a Calicivirus upon Interaction with Its Functional Receptor

2010 ◽  
Vol 84 (11) ◽  
pp. 5550-5564 ◽  
Author(s):  
Robert J. Ossiboff ◽  
Yi Zhou ◽  
Patrick J. Lightfoot ◽  
B. V. Venkataram Prasad ◽  
John S. L. Parker
Keyword(s):  
Conformational Changes ◽  
Viral Entry ◽  
Structural Changes ◽  
Feline Calicivirus ◽  
Soluble Receptor ◽  
Viral Capsids ◽  
Dimer Interface ◽  
Metastable Structures ◽  
Growth Properties ◽  
Functional Receptor

ABSTRACT Nonenveloped viral capsids are metastable structures that undergo conformational changes during virus entry that lead to interactions of the capsid or capsid fragments with the cell membrane. For members of the Caliciviridae, neither the nature of these structural changes in the capsid nor the factor(s) responsible for inducing these changes is known. Feline junctional adhesion molecule A (fJAM-A) mediates the attachment and infectious viral entry of feline calicivirus (FCV). Here, we show that the infectivity of some FCV isolates is neutralized following incubation with the soluble receptor at 37°C. We used this property to select mutants resistant to preincubation with the soluble receptor. We isolated and sequenced 24 soluble receptor-resistant (srr) mutants and characterized the growth properties and receptor-binding activities of eight mutants. The location of the mutations within the capsid structure of FCV was mapped using a new 3.6-Å structure of native FCV. The srr mutations mapped to the surface of the P2 domain were buried at the protruding domain dimer interface or were present in inaccessible regions of the capsid protein. Coupled with data showing that both the parental FCV and the srr mutants underwent increases in hydrophobicity upon incubation with the soluble receptor at 37°C, these findings indicate that FCV likely undergoes conformational change upon interaction with its receptor. Changes in FCV capsid conformation following its interaction with fJAM-A may be important for subsequent interactions of the capsid with cellular membranes, membrane penetration, and genome delivery.

scholarly journals Structural changes in DNA-binding proteins on complexation

2018 ◽  
Vol 46 (7) ◽  
pp. 3298-3308 ◽  
Author(s):  
Sayan Poddar ◽  
Devlina Chakravarty ◽  
Pinak Chakrabarti
Keyword(s):  
Dna Binding ◽  
Structural Changes ◽  
Binding Proteins ◽  
Dna Binding Proteins

scholarly journals TFIIA induces conformational changes in TFIID via interactions with the basic repeat.

1992 ◽  
Vol 12 (11) ◽  
pp. 5189-5196 ◽  
Author(s):  
D K Lee ◽  
J DeJong ◽  
S Hashimoto ◽  
M Horikoshi ◽  
R G Roeder
Keyword(s):  
Dna Binding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Inhibitory Effect ◽  
Binding Studies ◽  
Binding Interaction ◽  
Contact Points ◽  
Tata Element ◽  
N Terminus ◽  
Dna Binding Studies

DNA-binding studies with Saccharomyces cerevisiae TFIID point mutants indicated that TFIIA interacts with the basic repeat region of TFIID and induces structural changes. The latter was shown by the ability of TFIIA to compensate for TFIID point mutants defective for DNA binding. Interaction with TFIIA also rendered TFIID binding temperature independent, thus mimicking the effect of removing the nonconserved N terminus of TFIID. In addition, N-terminal truncation of the TFIID point mutants defective for DNA binding mimicked the ability of TFIIA to restore DNA binding of those mutants. Taken together, these results suggest that TFIIA enhances TFIID binding to DNA by eliminating an otherwise inhibitory effect of the nonconserved N terminus of TFIID. Furthermore, analyses of TFIID contact points on DNA and binding studies with TATA-containing oligonucleotide probes showed that TFIIA decreases the effect of sequences flanking the adenovirus major late TATA element on TFIID binding to DNA, suggesting a possible role of TFIIA in allowing TFIID to recognize a wider variety of promoters.

Engineered improvements in DNA-binding function of the MATa1 homeodomain reveal structural changes involved in combinatorial control

2002 ◽  
Vol 316 (2) ◽  
pp. 247-256 ◽  
Author(s):  
Beverly Hart ◽  
Jonathan R Mathias ◽  
David Ott ◽  
Lynn McNaughton ◽  
Janet S Anderson ◽  
...  
Keyword(s):  
Dna Binding ◽  
Structural Changes ◽  
Binding Function ◽  
Combinatorial Control

scholarly journals Asymmetric arginine dimethylation of RelA provides a repressive mark to modulate TNFα/NF-κB response

2016 ◽  
Vol 113 (16) ◽  
pp. 4326-4331 ◽  
Author(s):  
Anja Reintjes ◽  
Julian E. Fuchs ◽  
Leopold Kremser ◽  
Herbert H. Lindner ◽  
Klaus R. Liedl ◽  
...  
Keyword(s):  
Dna Binding ◽  
Stress Responses ◽  
Structural Changes ◽  
Target Genes ◽  
Direct Interaction ◽  
Type I ◽  
Critical Residue ◽  
The Stability ◽  
Dynamics Simulations ◽  
Protein Arginine Methyltransferase 1

Nuclear factor kappa B (NF-κB) is an inducible transcription factor that plays critical roles in immune and stress responses and is often implicated in pathologies, including chronic inflammation and cancer. Although much has been learned about NF-κB–activating pathways, the specific repression of NF-κB is far less well understood. Here we identified the type I protein arginine methyltransferase 1 (PRMT1) as a restrictive factor controlling TNFα-induced activation of NF-κB. PRMT1 forms a cellular complex with NF-κB through direct interaction with the Rel homology domain of RelA. We demonstrate that PRMT1 methylates RelA at evolutionary conserved R30, located in the DNA-binding L1 loop, which is a critical residue required for DNA binding. Asymmetric R30 dimethylation inhibits the binding of RelA to DNA and represses NF-κB target genes in response to TNFα. Molecular dynamics simulations of the DNA-bound RelA:p50 predicted structural changes in RelA caused by R30 methylation or a mutation that interferes with the stability of the DNA–NF-κB complex. Our findings provide evidence for the asymmetric arginine dimethylation of RelA and unveil a unique mechanism controlling TNFα/NF-κB signaling.

scholarly journals Residue R113 Is Essential for PhoP Dimerization and Function: a Residue Buried in the Asymmetric PhoP Dimer Interface Determined in the PhoPN Three-Dimensional Crystal Structure

2003 ◽  
Vol 185 (1) ◽  
pp. 262-273 ◽  
Author(s):  
Yinghua Chen ◽  
Catherine Birck ◽  
Jean-Pierre Samama ◽  
F. Marion Hulett
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Salt Bridge ◽  
Pho Regulon ◽  
Dimer Interface ◽  
And Function ◽  
Negative Phenotype

ABSTRACT Bacillus subtilis PhoP is a member of the OmpR/PhoB family of response regulators that is directly required for transcriptional activation or repression of Pho regulon genes in conditions under which Pi is growth limiting. Characterization of the PhoP protein has established that phosphorylation of the protein is not essential for PhoP dimerization or DNA binding but is essential for transcriptional regulation of Pho regulon genes. DNA footprinting studies of PhoP-regulated promoters showed that there was cooperative binding between PhoP dimers at PhoP-activated promoters and/or extensive PhoP oligomerization 3′ of PhoP-binding consensus repeats in PhoP-repressed promoters. The crystal structure of PhoPN described in the accompanying paper revealed that the dimer interface between two PhoP monomers involves nonidentical surfaces such that each monomer in a dimer retains a second surface that is available for further oligomerization. A salt bridge between R113 on one monomer and D60 on another monomer was judged to be of major importance in the protein-protein interaction. We describe the consequences of mutation of the PhoP R113 codon to a glutamate or alanine codon and mutation of the PhoP D60 codon to a lysine codon. In vivo expression of either PhoPR113E, PhoPR113A, or PhoPD60K resulted in a Pho-negative phenotype. In vitro analysis showed that PhoPR113E was phosphorylated by PhoR (the cognate histidine kinase) but was unable to dimerize. Monomeric PhoPR113E∼P was deficient in DNA binding, contributing to the PhoPR113E in vivo Pho-negative phenotype. While previous studies emphasized that phosphorylation was essential for PhoP function, data reported here indicate that phosphorylation is not sufficient as PhoP dimerization or oligomerization is also essential. Our data support the physiological relevance of the residues of the asymmetric dimer interface in PhoP dimerization and function.

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