| expression of a 434:vp16 chimeric activator leads to high-level activation of gene expression in stable transformants of arabidopsis. | the performance of an expression system based on a fusion of the bacteriophage 434-repressor to the vp16 activation domain of herpes simplex virus type 1 (434:vp16) was tested after stable integration into arabidopsis. a special feature of this system was the use of the monocot maize ubiquitin1 and rice actin1 promoters to drive the expression of the 434:vp16 activator and 434-repressor, respectively. our results demonstrate that the maize ubiquitin1 and the rice actin1 promoters, each of which ... | 2002 | 12054349 |
| isolation of altered specificity mutants of the single-chain 434 repressor that recognize asymmetric dna sequences containing the ttaa and ttac subsites. | a novel single-chain (sc) protein framework containing covalently dimerized dna-binding domains (dbd) of the phage 434 repressor was used to construct combinatorial mutant libraries in order to isolate mutant dbds with altered specificities. the library members contain one wild-type dbd and one mutant domain with randomized amino acids in the dna-contacting region. based on previous studies, the mutant sc derivatives are expected to recognize a general acaa-6 bp-nnnn sequence, where acaa is cont ... | 1999 | 10446235 |
| 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 ... | 2012 | 22755602 |
| ab initio prediction of helical segments in polypeptides. | an ab initio method has been developed to predict helix formation for polypeptides. the approach relies on the systematic analysis of overlapping oligopeptides to determine the helical propensity for individual residues. detailed atomistic level modeling, including entropic contributions, and solvation/ionization energies calculated through the solution of the poisson-boltzmann equation, is utilized. the calculation of probabilities for helix formation is based on the generation of ensembles of ... | 2002 | 11924737 |
| operator recognition by the phage 434 ci repressor: md simulations of free and bound 50-bp dna reveal important differences between the or1 and or2 sites. | using molecular dynamics simulations in explicit solvent, we investigated the behavior of a 50-bp dna sequence containing the 434 bacteriophage operators or1 and or2 separated by an 8-bp spacer. two simulations of 1 ns each were carried out, with dna alone and with dna complexed to dimers of the r1-69 dna binding domain of the phage 434 ci repressor protein at the or1 and or2 sites. strong correlations among average structural parameters are observed between our simulations and available experim ... | 2003 | 12548627 |
| dna-stimulated assembly of oligomeric bacteriophage 434 repressor: evidence for cooperative binding by recruitment. | typical of many transcriptional regulatory proteins, the lambdoid bacteriophage repressors bind cooperatively to multiple sites on dna. this cooperative binding is essential for establishment and maintenance of phage lysogeny. in the phage, two repressor homodimers, one bound at each of the adjacent operator sites, interact to form the tetramer that is necessary for the cooperative binding of the repressor. bacteriophage 434 repressor does not form tetramers in the absence of dna, and the mechan ... | 2003 | 12680780 |
| the preferred substrate for reca-mediated cleavage of bacteriophage 434 repressor is the dna-bound dimer. | induction of a lysogen of a lambdoid bacteriophage usually involves reca-stimulated autoproteolysis of the bacteriophage repressor protein. previous work on the phage repressors showed that the monomeric form of the protein is the target of reca. our previous work indicated that in the case of bacteriophage 434, virtually none of the repressor is present as a monomer in vivo. hence, if the repressor in a lysogen is present as a dimer, how can reca-stimulated autoproteolysis play a role in bacter ... | 2004 | 14679217 |
| 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 ... | 2004 | 15518542 |
| 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 ... | 2005 | 16077107 |
| 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 ... | 2001 | 18726407 |
| 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 ... | 2014 | 24710319 |