scholarly journals Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex

2019 ◽  
Vol 47 (13) ◽  
pp. 7118-7129 ◽  
Author(s):  
Branwen M Hall ◽  
Sue A Roberts ◽  
Matthew H J Cordes
Keyword(s):  
Binding Site ◽  
Protein Dimers ◽  
Dimerization Interface ◽  
Cro Protein ◽  
One To One ◽  
Induced Changes ◽  
Regulatory Dna ◽  
Van Der Waals Contacts ◽  
Site Binding ◽  
Cocrystal Structure

Abstract The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein–DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.

Phosphate Binding to Isolated Chloroplast Coupling Factor (CF1)

1988 ◽  
Vol 43 (3-4) ◽  
pp. 213-218 ◽  
Author(s):  
Bernhard Huchzermeyer
Keyword(s):  
Atpase Activity ◽  
Binding Site ◽  
Inorganic Phosphate ◽  
Coupling Factor ◽  
Binding Domain ◽  
Atp Binding ◽  
Phosphate Binding ◽  
Chloroplast Coupling Factor ◽  
Single Binding Site ◽  
Site Binding

A single binding site for phosphate was found on isolated chloroplast coupling factor in the absence of nucleotides. In our experiments the phosphate binding site showed a Kd of 170 μᴍ. We did not observe any differences whether the ATPase activity of CF] had been activated or not. If the enzyme was incubated with [γ-32P]ATP the amount of 32P bound per CF1 depended on the pretreatment of the enzyme: In the presence of ADP no ATP or phosphate was bound to CF,. After activation of ATPase activity one mol of ATP per mol CF, was rapidly bound and hydrolyzed while there was a slowly occurring binding of another phosphate without concomitant nucleotide binding. We conclude that there are two different types of phosphate binding observed in our experiments: 1) Inorganic phosphate can be bound by one catalytic site per mol of CF1 2) The γ-phosphate of ATP is able to bind to an ATP binding domain of the enzyme if this domain can exchange substrates with the incubation medium. This ATP binding domain appears to differ from the site binding inorganic phosphate, because at least a portion of the coupling factor contains more than one labelled phosphate during our ATPase tests.

scholarly journals SiteOut: an online tool to design binding site-free DNA sequences

2015 ◽  
Author(s):  
Javier Estrada ◽  
Teresa Ruiz-Herrero ◽  
Clarissa Scholes ◽  
Zeba Wunderlich ◽  
Angela DePace
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Binding Sites ◽  
Regulatory Proteins ◽  
Biological Processes ◽  
Major Goal ◽  
Specific Sequence ◽  
Online Tool ◽  
Protein Binding Sites ◽  
Regulatory Dna

DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/

scholarly journals The Zinc-Dependent Major Histocompatibility Complex Class II Binding Site of Streptococcal Pyrogenic Exotoxin C Is Critical for Maximal Superantigen Function and Toxic Activity

2003 ◽  
Vol 71 (3) ◽  
pp. 1548-1550 ◽  
Author(s):  
Timothy J. Tripp ◽  
John K. McCormick ◽  
Jennifer M. Webb ◽  
Patrick M. Schlievert
Keyword(s):  
Major Histocompatibility Complex ◽  
Binding Site ◽  
Biological Function ◽  
Biological Activities ◽  
Major Histocompatibility ◽  
Toxic Activity ◽  
Histocompatibility Complex ◽  
Β Chain ◽  
Cocrystal Structure ◽  
Dependent Interaction

ABSTRACT The cocrystal structure of streptococcal pyrogenic exotoxin C (SPE C) with HLA-DR2a (DRA*0101,DRB5*0101) revealed a zinc-dependent interaction site through residues 167, 201, and 203 on SPE C and residue 81 on the β-chain of HLA-DR2a (DRA*0101,DRB5*0101). Mutation of these SPE C residues resulted in dramatically reduced biological activities. Thus, the zinc-dependent major histocompatibility complex II binding site is critical for maximal biological function of SPE C.

scholarly journals Enhanced TF binding site maps improve regulatory networks learned from accessible chromatin data

2019 ◽  
Author(s):  
Shubhada R. Kulkarni ◽  
D. Marc Jones ◽  
Klaas Vandepoele
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Regulatory Networks ◽  
Transcriptional Control ◽  
Chromatin Accessibility ◽  
Systematic Evaluation ◽  
Open Chromatin ◽  
Ensemble Approach ◽  
Complete Cell ◽  
Regulatory Dna

ABSTRACTDetermining where transcription factors (TF) bind in genomes provides insights into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these datasets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF binding preferences, or motifs, to identify TF binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here we compare four motif mapping tools widely used in the Arabidopsis research community and evaluate their performance using chromatin immunoprecipitation datasets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of FIMO, one of the most frequently used motif mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a new protocol is presented to efficiently derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression datasets.

scholarly journals Activation of the Redox-regulated Chaperone Hsp33 by Domain Unfolding

2004 ◽  
Vol 279 (19) ◽  
pp. 20529-20538 ◽  
Author(s):  
Paul C. F. Graf ◽  
Maria Martinez-Yamout ◽  
Stephen VanHaerents ◽  
Hauke Lilie ◽  
H. Jane Dyson ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Binding Site ◽  
Conformational Changes ◽  
Substrate Binding ◽  
Helical Structure ◽  
Activation Process ◽  
Spectroscopic Techniques ◽  
Substrate Binding Site ◽  
C Terminus ◽  
Dimerization Interface

The molecular chaperone Hsp33 inEscherichia coliresponds to oxidative stress conditions with the rapid activation of its chaperone function. On its activation pathway, Hsp33 progresses through three major conformations, starting as a reduced, zinc-bound inactive monomer, proceeding through an oxidized zinc-free monomer, and ending as a fully active oxidized dimer. While it is known that Hsp33 senses oxidative stress through its C-terminal four-cysteine zinc center, the nature of the conformational changes in Hsp33 that must take place to accommodate this activation process is largely unknown. To investigate these conformational rearrangements, we constructed constitutively monomeric Hsp33 variants as well as fragments consisting of the redox regulatory C-terminal domain of Hsp33. These proteins were studied by a combination of biochemical and NMR spectroscopic techniques. We found that in the reduced, monomeric conformation, zinc binding stabilizes the C terminus of Hsp33 in a highly compact, α-helical structure. This appears to conceal both the substrate-binding site as well as the dimerization interface. Zinc release without formation of the two native disulfide bonds causes the partial unfolding of the C terminus of Hsp33. This is sufficient to unmask the substrate-binding site, but not the dimerization interface, rendering reduced zinc-free Hsp33 partially active yet monomeric. Critical for the dimerization is disulfide bond formation, which causes the further unfolding of the C terminus of Hsp3 and allows the association of two oxidized Hsp33 monomers. This then leads to the formation of active Hsp33 dimers, which are capable of protecting cells against the severe consequences of oxidative heat stress.

scholarly journals Binding of aldolase to actin-containing filaments. Quantitative reappraisal of the interactions

1981 ◽  
Vol 195 (1) ◽  
pp. 297-299 ◽  
Author(s):  
C J Masters ◽  
D J Winzor ◽  
L W Nichol
Keyword(s):  
Theoretical Analysis ◽  
Binding Site ◽  
Binding Sites ◽  
Binding Constant ◽  
Thin Filament ◽  
Repeat Unit ◽  
Cross Linking ◽  
A Value ◽  
Equilibrium Partition ◽  
Site Binding

Previously reported results of equilibrium-partition experiments on the interaction of aldolase with actin-containing filaments [Walsh, Winzor, Clarke, Masters & Morton (1980) Biochem. J. 186, 89-98] have been subjected to a more rigorous theoretical analysis involving consideration of the consequences of cross-linking interactions between enzyme and filament. The experimental results obtained with F-actin-tropomyosin are best described by a model with one binding site per heptameric repeat unit of filament and a value of 39000 M-1 for the site binding constant, k. Similar analyses of the influence of Ca2+ on aldolase binding to F-actin--tropomyosin--troponin substantiate the existence of two equivalent binding sites (k = 14900 M-1) for the enzyme on each repeat unit of the thin filament. The Ca2+-sensitivity of this interaction reflects either a decrease in the strength of aldolase binding to these two sites (k = 8200 M-1) or the elimination of one site.

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