Abstract：
:Fundamental biological processes require concurrent sharing of DNA by numerous motor proteins and complexes. Thus, collision, congestion, and roadblocks are inescapable on these busy "molecular highways." The consequences of these traffic problems are diverse, resulting in complex cellular mechanisms to resolve threats to genome stability and ensure cellular viability. Here, we review the different types of events and the diverse consequences that an RNA polymerase may encounter during transcription. We also address advances in the field that facilitate in-depth investigation of intrinsic motor properties and multi-protein interactions and coordination, which are necessary to understand these complicated interactions. Together, these results provide mechanistic insights into how RNA polymerase successfully navigates its passage through crowded molecular highways.
journal_name
J Mol Bioljournal_title
Journal of molecular biologyauthors
Le TT,Wang MDdoi
10.1016/j.jmb.2018.08.006subject
Has Abstractpub_date
2018-10-26 00:00:00pages
4513-4524issue
22eissn
0022-2836issn
1089-8638pii
S0022-2836(18)30914-8journal_volume
430pub_type
杂志文章,评审abstract：:Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-re...
journal_title：Journal of molecular biology
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abstract：:Calmodulin (CaM) is a ubiquitous second messenger protein that regulates a variety of structurally and functionally diverse targets in response to changes in Ca(2+) concentration. CaM-dependent protein kinase II (CaMKII) and calcineurin (CaN) are the prominent CaM targets that play an opposing role in many cellular fu...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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abstract：:Rvb1 and Rvb2 are essential AAA(+) (ATPases associated with diverse cellular activities) helicases, which are important components of critical complexes such as chromatin remodeling and telomerase complexes. The oligomeric state of the Rvb proteins has been controversial. Independent studies from several groups have d...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2010.10.003
更新日期：2010-12-03 00:00:00
abstract：:EmrE is a bacterial multidrug transporter of the small multidrug resistance family, which extrudes large hydrophobic cations such as tetraphenylphosphonium (TPP(+)) out of the cell by a proton antiport mechanism. Binding measurements were performed on purified EmrE solubilized in dodecylmaltoside to determine the stoi...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(03)00895-7
更新日期：2003-09-05 00:00:00
abstract：:Single crystals of a multienzyme complex isolated from spinach leaves, and containing RUBISCO bound to the substrate RuBP have been grown and characterized. The crystals belong to the orthorhombic space group P2(1)2(1)2 with a = 173 A, b = 134 A and c = 112 A, and contain two enzyme complex molecules in the unit cell....
journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：1993-12-20 00:00:00
abstract：:The high resolution structures of bovine pancreatic trypsin inhibitor refined in two distinct crystal forms have been compared. One of the structures was a result of new least-squares X-ray refinement of data from crystal form I, while the other was the joint X-ray/neutron structure of crystal form II. After superposi...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2008.07.007
更新日期：2008-10-03 00:00:00
abstract：:We investigate the conservation of amino acid residue sequences in 21 DNA-binding protein families and study the effects that mutations have on DNA-sequence recognition. The observations are best understood by assigning each protein family to one of three classes: (i) non-specific, where binding is independent of DNA ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/s0022-2836(02)00571-5
更新日期：2002-07-26 00:00:00
abstract：:The effects of RNA methylation on HIV-1 replication remain largely unknown. Recent studies have discovered new insights into the effect of 2'-O-methylation and 5-methylcytidine marks on the HIV-1 RNA genome. As so far, HIV-1 benefits from diverse RNA methylations through distinct mechanisms. In this review, we summari...
journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2019.09.021
更新日期：2019-12-06 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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journal_title：Journal of molecular biology
pub_type： 杂志文章,评审
doi：10.1016/j.jmb.2018.06.031
更新日期：2018-11-02 00:00:00
abstract：:We have recently reported a novel human repetitive DNA (Sau3A family) that exists both in the chromosomes and in the extrachromosomal fraction. Several more clones that hybridized with the Sau3A family were isolated from the extrachromosomal fraction of HeLa cells. Use of these clones as probes has revealed that at le...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(87)90342-1
更新日期：1987-02-20 00:00:00
abstract：:Polyamines are abundant metabolites that directly influence gene expression. Although the role of polyamines in DNA condensation is well known, their role in RNA folding is less understood. Non-denaturing gel electrophoresis was used to monitor the equilibrium folding transitions of the Tetrahymena ribozyme in the pre...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2004.06.008
更新日期：2004-07-30 00:00:00
abstract：:A hallmark of the catalytically essential Walker B motif of P-loop NTPases is the presence of an acidic residue (aspartate/glutamate) for efficient Mg2+ coordination. Although the Walker B motif has been identified in well-studied examples of P-loop NTPases, its identity is ambiguous in many families, for example, in ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2020.07.024
更新日期：2020-09-18 00:00:00
abstract：:The Hippo pathway plays a crucial role in growth control, proliferation and tumor suppression. Activity of the signaling pathway is associated with cell density sensing and tissue organization. Furthermore, the Hippo pathway helps to coordinate cellular processes through crosstalk with growth-factor-mediated signaling...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2015.04.015
更新日期：2015-10-23 00:00:00
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journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0826
更新日期：1997-03-21 00:00:00
abstract：:Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 angstroms in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/j.jmb.2005.10.048
更新日期：2006-01-13 00:00:00
abstract：:The vicinal amide proton-C alpha proton spin-spin coupling constants, JHN alpha, in the globular protein basic pancreatic trypsin inhibitor (BPTI) have been measured using phase-sensitive correlated spectroscopy at high digital resolution. In conjunction with the crystal structure of BPTI, these data were used to cali...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1016/0022-2836(84)90035-4
更新日期：1984-12-15 00:00:00
abstract：:DNA replication fork arrest during the termination phase of chromosome replication in Bacillus subtilis is brought about by the replication terminator protein (RTP) bound to specific DNA terminator sequences (Ter sites) distributed throughout the terminus region. An attractive suggestion by others was that crucial to ...
journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：1999-03-12 00:00:00
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journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
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journal_title：Journal of molecular biology
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pub_type： 杂志文章
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journal_title：Journal of molecular biology
pub_type： 杂志文章
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更新日期：2005-07-29 00:00:00
abstract：:The catalytic or functionally important residues of a protein are known to exist in evolutionarily constrained regions. However, the patterns of residue conservation alone are sometimes not very informative, depending on the homologous sequences available for a given query protein. Here, we present an integrated metho...
journal_title：Journal of molecular biology
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更新日期：2003-04-11 00:00:00
abstract：:The pyrogenic toxin toxic shock syndrome toxin-1 from Staphylococcus aureus is a causative agent of the toxic shock syndrome disease. It belongs to a family of proteins known as superantigens that cross-link major histocompatibility class II molecules and T-cell receptors leading to the activation of a substantial num...
journal_title：Journal of molecular biology
pub_type： 杂志文章
doi：10.1006/jmbi.1996.0421
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