The Experts below are selected from a list of 27021 Experts worldwide ranked by ideXlab platform
David Cowburn - One of the best experts on this subject based on the ideXlab platform.
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Structural and dynamical features of inteins and implications on protein splicing.
The Journal of biological chemistry, 2014Co-Authors: Ertan Eryilmaz, Neel H. Shah, Tom W. Muir, David CowburnAbstract:Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microorganisms from all domains of life. Despite this broad phylogenetic distribution, all inteins share common structural features such as a horseshoe-like pseudo two-fold symmetric fold, several Canonical Sequence motifs, and similar splicing mechanisms. Intriguingly, the splicing efficiencies and substrate specificity of different inteins vary considerably, reflecting subtle changes in the chemical mechanism of splicing, linked to their local structure and dynamics. As intein chemistry has widespread use in protein chemistry, understanding the structural and dynamical aspects of inteins is crucial for intein engineering and the improvement of intein-based technologies.
David A Brian - One of the best experts on this subject based on the ideXlab platform.
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downstream Sequences influence the choice between a naturally occurring nonCanonical and closely positioned upstream Canonical heptameric fusion motif during bovine coronavirus subgenomic mrna synthesis
Journal of Virology, 2001Co-Authors: Aykut Ozdarendeli, Sylvie Rochat, Gwyn D Williams, Savithra D Senanayake, David A BrianAbstract:Mechanisms leading to subgenomic mRNA (sgmRNA) synthesis in coronaviruses are poorly understood but are known to involve a heptameric signaling motif, originally called the intergenic Sequence. The intergenic Sequence is the presumed crossover region (fusion site) for RNA-dependent RNA polymerase (RdRp) during discontinuous transcription, a process leading to sgmRNAs that are both 5′ and 3′ coterminal. In the bovine coronavirus, the major fusion site for synthesis of mRNA 5 (GGUAGAC) does not conform to the Canonical motif (UC[U,C]AAAC) at three positions (underlined), yet it lies just 14 nucleotides downstream from such a Sequence (UCCAAAC). The infrequently used Canonical Sequence, by computer prediction, is buried within the stem of a stable hairpin (−17.2 kcal/mol). Here we document the existence of this stem by enzyme probing and examine its influence and that of neighboring Sequences on the unusual choice of fusion sites by analyzing transcripts made in vivo from mutated defective interfering RNA constructs. We learned that (i) mutations that were predicted to unfold the stem-loop in various ways did not switch RdRp crossover to the upstream Canonical site, (ii) a totally nonconforming downstream motif resulted in no measurable transcription from either site, (iii) the Canonical upstream site does not function ectopically to lend competence to the downstream nonCanonical site, and (iv) altering flanking Sequences downstream of the downstream nonCanonical motif in ways that diminish Sequence similarity with the virus genome 5′ end caused a dramatic switch to the upstream Canonical site. These results show that Sequence elements downstream of the nonCanonical site can dramatically influence the choice of fusion sites for synthesis of mRNA 5 and are interpreted as being most consistent with a mechanism of similarity-assisted RdRp strand switching during minus-strand synthesis.
Vassilios Fessatidis - One of the best experts on this subject based on the ideXlab platform.
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Ground-state energy of a two level system with phonon coupling
Physics Letters A, 2012Co-Authors: Vassilios Fessatidis, Jay D. Mancini, William J. Massano, Frank A. Corvino, Samuel P. BowenAbstract:Abstract The coupling of a two-level system to quantized boson modes has been the focus of many researchers for a number of years. Applications to exciton motion, molecular polaron formation, chaos in quantum systems as well as a number of other effects in condensed matter physics have also been studied. Here we investigate the interaction of bosonic modes with a two-level fermionic system. This quantum system is used as a testing ground for a recently developed Generalized Moments Expansion, GMX ( m , n ) , of which the well-known Connected Moments Expansion (CMX) and Alternate Moments Expansion (AMX) are special cases. The convergence and viability of this scheme are discussed and comparisons are made with a related Canonical Sequence Method (CSM) as well as a Lanczos tridiagonal truncation scheme.
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Zero point energy of the Pullen–Edmonds Hamiltonian
Journal of Mathematical Chemistry, 2008Co-Authors: Vassilios Fessatidis, Jay D. Mancini, Samuel P. Bowen, Mauricio CampuzanoAbstract:Here we wish to apply the newly developed Generalized Moments Expansion (GMX) to the well-known potential $$U(x, y) = \frac{1}{2}\left( x^{2}+y^{2}\right) + \alpha x^{2}y^{2},$$ which is used to model such molecular systems as formamide (HCONH_2) and carbon suboxide (C_3O_2). Our motivation is to investigate the numerical accuracy as well as the viability of the GMX for evaluating ground-state energies of quantum Hamiltonian systems. The zero-point energy of this potential is calculated and results are compared to those of a related Canonical Sequence Method approach (CSM).
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Canonical Sequence method applied to a two-dimensional spin system
Physics Letters A, 2008Co-Authors: Vassilios Fessatidis, Jay D. Mancini, Samuel P. BowenAbstract:A number of years ago, Horn and Weinstein introduced a novel nonperturbative method, the t-expansion, for calculating ground-state expectation values for Hamiltonian systems. Recently Samaj et al. have generalized the t-expansion technique and the related connected moments expansion to a more general Canonical Sequence. In the present work we have expounded upon this work and have applied this to the two-dimensional square anisotropic XXZ Heisenberg model.
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Correlation energy of a model problem
Physics Letters A, 2006Co-Authors: Vassilios Fessatidis, Jay D. Mancini, Samuel P. Bowen, Mauricio CampuzanoAbstract:Abstract A newly derived generalized moments expansion (GMX), based on the “ t -expansion” of Horn and Weinstein, is used to calculate the correlation energy of a model Hamiltonian representing N coupled one-dimensional harmonic oscillators. Comparisons are made with a related calculational scheme the Canonical Sequence method (CSM).
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Correction energy of water and hydrogen fluoride
Physics Letters A, 2005Co-Authors: Jay D. Mancini, Vassilios Fessatidis, Samuel P. BowenAbstract:We wish to study the correction energy of water and hydrogen fluoride (HF) using the recently developed Canonical Sequence method (CSM) which is a calculational cousin of the connected moments expansion (CMX) of Cioslowski. Comparisons are then made with other methods [for example, P.J. Knowles, Chem. Phys. Lett. 134 (1987) 512].
George M. Stancel - One of the best experts on this subject based on the ideXlab platform.
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the 3 flanking region of the mouse c fos gene contains a cluster of ggtca hormone response like elements
Molecular Biology Reports, 1998Co-Authors: Salman M. Hyder, Constance Chiappetta, George M. StancelAbstract:We previously identified an estrogen response element in the 3′-flanking region of the c-fos protooncogene [1, 2]. This element, GGTCAnnnCAGCC, has one half-site identical to that of the consensus ERE (GGTCAnnnTGACC) but only limited homology to the second half-site. Because of this non-Canonical Sequence and atypical location in the 3′-untranslated region of an estrogen target gene, we decided to analyze Sequences adjacent to this element for the possible presence of other regulatory elements. We now report that the 635 base pairs downstream of the c-fos ERE contain: (i) an unusual cluster of 7 GGTCA hormone response-like elements; (ii) potential binding sites for other known DNA binding proteins; and (iii) a Sequence specific binding site for a non-estrogen receptor protein present in hormone target tissues.
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the 3 flanking region of the mouse c fos gene contains a cluster of ggtca hormone response like elements
Molecular Biology Reports, 1998Co-Authors: Salman M. Hyder, Constance Chiappetta, George M. StancelAbstract:We previously identified an estrogen response element in the 3′-flanking region of the c-fos protooncogene [1, 2]. This element, GGTCAnnnCAGCC, has one half-site identical to that of the consensus ERE (GGTCAnnnTGACC) but only limited homology to the second half-site. Because of this non-Canonical Sequence and atypical location in the 3′-untranslated region of an estrogen target gene, we decided to analyze Sequences adjacent to this element for the possible presence of other regulatory elements. We now report that the 635 base pairs downstream of the c-fos ERE contain: (i) an unusual cluster of 7 GGTCA hormone response-like elements; (ii) potential binding sites for other known DNA binding proteins; and (iii) a Sequence specific binding site for a non-estrogen receptor protein present in hormone target tissues.
Ertan Eryilmaz - One of the best experts on this subject based on the ideXlab platform.
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Structural and dynamical features of inteins and implications on protein splicing.
The Journal of biological chemistry, 2014Co-Authors: Ertan Eryilmaz, Neel H. Shah, Tom W. Muir, David CowburnAbstract:Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microorganisms from all domains of life. Despite this broad phylogenetic distribution, all inteins share common structural features such as a horseshoe-like pseudo two-fold symmetric fold, several Canonical Sequence motifs, and similar splicing mechanisms. Intriguingly, the splicing efficiencies and substrate specificity of different inteins vary considerably, reflecting subtle changes in the chemical mechanism of splicing, linked to their local structure and dynamics. As intein chemistry has widespread use in protein chemistry, understanding the structural and dynamical aspects of inteins is crucial for intein engineering and the improvement of intein-based technologies.