monovalent cations regulate dna sequence recognition by 434 repressor.the bacteriophage 434 repressor distinguishes between its six naturally occurring binding sites using indirect readout. in indirect readout, sequence-dependent differences in the structure and flexibility of non-contacted bases in a protein's dna-binding site modulate the affinity of dna for protein. the conformation and flexibility of a dna sequence can be influenced by the interaction of the dna bases or backbone with solution components. we examined the effect of changing the cation-type pres ...200415210346
dna-mediated assembly of weakly interacting dna-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast gcn4 dna-binding domains.the specificity of dna-mediated protein assembly was studied in two in vitro systems, based on (i) the dna-binding domain of bacteriophage 434 repressor ci (amino acid residues 1-69), or (ii) the dna-binding domain of the yeast transcription factor gcn4, (amino acids 1-34) and their respective oligonucleotide cognates. in vivo, both of these peptides are part of larger protein molecules that also contain dimerization domains, and the resulting dimers recognize cognate palindromic dna sequences t ...200415388801
nmr structures of salt-refolded forms of the 434-repressor dna-binding domain in 6 m urea.the n-terminal 63-residue fragment of the phage 434-repressor, 434(1-63), has a well-defined globular fold in h(2)o solution, and is unfolded in 6 m urea at ph 7.5. in this study, 434(1-63) has been refolded by adding either 1.7 m nacl or 0.47 m natfa to the solution in 6 m urea, and the nmr structures of both refolded forms have been determined. the two refolded forms have similar free energies of unfolding and are approximately 16 kj/mol less stable than the protein in h(2)o solution. 434(1-63 ...200415518542
the bacteriophage 434 repressor dimer preferentially undergoes autoproteolysis by an intramolecular mechanism.inactivation of the lambdoid phage repressor protein is necessary to induce lytic growth of a lambdoid prophage. activated reca, the mediator of the host sos response to dna damage, causes inactivation of the repressor by stimulating the repressor's nascent autocleavage activity. the repressor of bacteriophage lambda and its homolog, lexa, preferentially undergo reca-stimulated autocleavage as free monomers, which requires that each monomer mediates its own (intramolecular) cleavage. the ci repr ...200516077107
information-driven protein-dna docking using haddock: it is a matter of flexibility.intrinsic flexibility of dna has hampered the development of efficient protein-dna docking methods. in this study we extend haddock (high ambiguity driven docking) [c. dominguez, r. boelens and a. m. j. j. bonvin (2003) j. am. chem. soc. 125, 1731-1737] to explicitly deal with dna flexibility. haddock uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. the latter allow for flexibility of all dna nucleo ...200616820531
indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different dna elastic potentials.essential biological processes require that proteins bind to a set of specific dna sites with tuned relative affinities. we focus on the indirect readout mechanism and discuss its theoretical description in relation to the present understanding of dna elasticity on the rigid base pair level. combining existing parametrizations of elastic potentials for dna, we derive elastic free energies directly related to competitive binding experiments, and propose a computationally inexpensive local marker ...200617038333
effect of salt shock on stability of lambdaimm434 lysogens.the affinities of the bacteriophage 434 repressor for its various binding sites depend on the type and/or concentration of monovalent cations. the ability of bacteriophage 434 repressor to govern the lysis-lysogeny decision depends on the dna binding activities of the phage's ci repressor protein. we wished to determine whether changes in the intracellular ionic environment influence the lysis-lysogeny decision of the bacteriophage lambda(imm434). our findings show that the ionic composition wit ...200717307857
selection and design of high affinity dna ligands for mutant single-chain derivatives of the bacteriophage 434 repressor.single-chain repressor rr(tres) is a derivative of bacteriophage 434 repressor, which contains covalently dimerized dna-binding domains (amino acids 1-69) of the phage 434 repressor. in this single-chain molecule, the wild type domain r is connected to the mutant domain r(tres) by a recombinant linker in a head-to-tail arrangement. the dna-contacting amino acids of r(tres) at the -1, 1, 2, and 5 positions of the a3 helix are t, r, e, s respectively. by using a randomized dna pool containing the ...200118726407
mechanisms that determine the differential stability of stx⁺ and stx(-) lysogens.phages 933w, baa2326, 434, and λ are evolutionarily-related temperate lambdoid phages that infect escherichia coli. although these are highly-similar phages, baa2326 and 933w naturally encode shiga toxin 2 (stx⁺), but phage 434 and λ do not (stx(-)). previous reports suggest that the 933w stx⁺ prophage forms less stable lysogens in e. coli than does the stx(-) prophages λ, p22, and 434. the higher spontaneous induction frequency of the stx⁺ prophage may be correlated with both virulence and disp ...201627043626
flexibility of the linker between the domains of dna methyltransferase ssoii revealed by small-angle x-ray scattering: implications for transcription regulation in ssoii restriction-modification system.(cytosine-5)-dna methyltransferase ssoii (m.ssoii) consists of a methyltransferase domain (residues 72-379) and an n-terminal region (residues 1-71) which regulates transcription in ssoii restriction-modification system. small-angle x-ray scattering (saxs) is employed here to study the low resolution structure of m.ssoii and its complex with dna containing the methylation site. the shapes reconstructed ab initio from the saxs data reveal two distinct protein domains of unequal size. the larger d ...201424710319
multiple molecule effects on the cooperativity of protein folding transitions in simulations.though molecular simulation of proteins has made notable contributions to the study of protein folding and kinetics, disagreement between simulation and experiment still exists. one of the criticisms levied against simulation is its failure to reproduce cooperative protein folding transitions. this weakness has been attributed to many factors such as a lack of polarizability and adequate capturing of solvent effects. this work, however, investigates how increasing the number of proteins simulate ...201222755602
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