Electrostatics and Self-Contact in an Elastic Rod Approximation for DNA

2010 ◽  
Vol 6 (1) ◽  
Author(s):  
Todd D. Lillian ◽  
N. C. Perkins
Keyword(s):  
Electrostatic Interactions ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Elastic Rod ◽  
Storage And Retrieval ◽  
Cellular Processes ◽  
The Stability ◽  
Straight Rod

Deoxyribonucleic acid (DNA) is an essential molecule that enables the storage and retrieval of genetic information. In its role during cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elastodynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions, which are essential when considering processes that result in highly supercoiled DNA including plectonemes. Herein, we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.

Electrostatics and Self Contact in an Elastic Rod Approximation for DNA

2009 ◽  
Author(s):  
Todd D. Lillian ◽  
N. C. Perkins
Keyword(s):  
Electrostatic Interactions ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Elastic Rod ◽  
Storage And Retrieval ◽  
Cellular Processes ◽  
The Stability ◽  
Straight Rod

DNA is a life-sustaining molecule that enables the storage and retrieval of genetic information. In its role during essential cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elasto-dynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions which are essential when considering processes that result in highly super-coiled DNA including plectonemes. Herein we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.

scholarly journals HU Protein and DNA Supercoiling Dramatically Enhance Lac-Repressor-Mediated DNA Looping

2016 ◽  
Vol 110 (3) ◽  
pp. 236a
Author(s):  
Yan Yan ◽  
Fenfei Leng ◽  
David D. Dunlap ◽  
Laura Finzi
Keyword(s):  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Hu Protein

scholarly journals Negative DNA supercoiling tunes protein-mediated looping

2021 ◽  
Author(s):  
Yan Yan ◽  
Wenxuan Xu ◽  
Sandip Kumar ◽  
Alexander Zhang ◽  
Fenfei Leng ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Emergent Behavior ◽  
Dna Looping ◽  
Inherent Feature ◽  
Loop Dynamics ◽  
Negative Supercoiling ◽  
Deterministic Behavior ◽  
Fundamental Mechanism

Protein-mediated DNA looping is a fundamental mechanism of gene regulation. Such loops occur stochastically, and a calibrated response to environmental stimuli would seem to require more deterministic behavior, so experiments were preformed to determine whether additional proteins and/or DNA supercoiling might be definitive. In experiments on DNA looping mediated by the Escherichia coli lac repressor protein, increasing compaction by the nucleoid-associated protein, HU, progressively increased the average looping probability for an ensemble of single molecules. Despite this trend, the looping probabilities associated with individual molecules ranged from 0 to 100 throughout the titration, and observations of a single molecule for an hour or longer were required to observe the statistical looping behavior of the ensemble, ergodicity. Increased negative supercoiling also increased the looping probability for an ensemble of molecules, but the looping probabilities of individual molecules more closely resembled the ensemble average. Furthermore, supercoiling accelerated the loop dynamics such that in as little as twelve minutes of observation most molecules exhibited the looping probability of the ensemble. Notably, this is within the timescale of the doubling time of the bacterium. DNA supercoiling, an inherent feature of genomes across kingdoms, appears to be a fundamental determinant of time-constrained, emergent behavior in otherwise random molecular activity.

scholarly journals Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase

2001 ◽  
Vol 14 (11) ◽  
pp. 911-917 ◽  
Author(s):  
Francesca Trejo ◽  
Josep Ll. Gelpí ◽  
Albert Ferrer ◽  
Albert Boronat ◽  
Montserrat Busquets ◽  
...  
Keyword(s):  
Malate Dehydrogenase ◽  
Electrostatic Interactions ◽  
The Stability ◽  
Cytosolic Malate Dehydrogenase

The search for formal electrostatic effects on molecular conformation and crystal packing: crystal structure of 2,2′′-disubstituted (HversusPPh2) 1,1′-(1,2-phenylene)bis(3-methyl-1H-imidazol-3-ium) bis(trifluoromethanesulfonate)

2016 ◽  
Vol 72 (3) ◽  
pp. 198-202
Author(s):  
Carine Duhayon ◽  
Yves Canac ◽  
Laurent Dubrulle ◽  
Carine Maaliki ◽  
Remi Chauvin
Keyword(s):  
Crystal Structure ◽  
Electrostatic Interactions ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Relative Orientation ◽  
Electron Delocalization ◽  
Electrostatic Effects ◽  
Conformational Freedom ◽  
The Stability ◽  
Bond Character

Electrostatic interactions between localized integral charges make the stability and structure of highly charged small and rigid organics intriguing. Can σ/π-electron delocalization compensate reduced conformational freedom by lowering the repulsion between identical charges? The crystal structure of the title salt, C14H16N42+·2CF3SO3−, (2), is described and compared with that of the 2,2′′-bis(diphenylphosphanyl) derivative, (4). The conformations of the dications and their interactions with neighbouring trifluoromethanesulfonate anions are first analyzed from the standpoint of formal electrostatic effects. Neither cation exhibits any geometrical strain induced by the intrinsic repulsion between the positive charges. In contrast, the relative orientation of the imidazolium rings [i.e. antifor (2) andsynfor (4)] is controlled by different configurations of the interactions with the closest trifluoromethanesulfonate anions. The long-range arrangement is also found to be specific: beyond the formal electrostatic packing, C—H...O and C—H...F contacts have no definite `hydrogen-bond' character but allow the delineation of layers, which are either pleated or flat in the packing of (2) or (4), respectively.

scholarly journals The Global Regulatory Cyclic AMP Receptor Protein (CRP) Controls Multifactorial Fluoroquinolone Susceptibility in Salmonella enterica Serovar Typhimurium

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Stefani C. Kary ◽  
Joshua R. K. Yoneda ◽  
Stephen C. Olshefsky ◽  
Laura A. Stewart ◽  
Steven B. West ◽  
...  
Keyword(s):  
Cyclic Amp ◽  
Salmonella Enterica ◽  
Topoisomerase I ◽  
Multiple Drug Resistance ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Receptor Protein ◽  
Multiple Drug ◽  
Topoisomerase Iv ◽  
Fluoroquinolone Antibiotics

ABSTRACT Fluoroquinolone antibiotics are prescribed for the treatment of Salmonella enterica infections, but resistance to this family of antibiotics is growing. Here we report that loss of the global regulatory protein cyclic AMP (cAMP) receptor protein (CRP) or its allosteric effector, cAMP, reduces susceptibility to fluoroquinolones. A Δcrp mutation was synergistic with the primary fluoroquinolone resistance allele gyrA83, thus able to contribute to clinically relevant resistance. Decreased susceptibility to fluoroquinolones could be partly explained by decreased expression of the outer membrane porin genes ompA and ompF with a concomitant increase in the expression of the ciprofloxacin resistance efflux pump gene acrB in Δcrp cells. Expression of gyrAB, which encode the DNA supercoiling enzyme GyrAB, which is blocked by fluoroquinolones, and expression of topA, which encodes the dominant supercoiling-relaxing enzyme topoisomerase I, were unchanged in Δcrp cells. Yet Δcrp cells maintained a more relaxed state of DNA supercoiling, correlating with an observed increase in topoisomerase IV (parCE) expression. Surprisingly, the Δcrp mutation had the unanticipated effect of enhancing fitness in the presence of fluoroquinolone antibiotics, which can be explained by the observation that exposure of Δcrp cells to ciprofloxacin had the counterintuitive effect of restoring wild-type levels of DNA supercoiling. Consistent with this, Δcrp cells did not become elongated or induce the SOS response when challenged with ciprofloxacin. These findings implicate the combined action of multiple drug resistance mechanisms in Δcrp cells: reduced permeability and elevated efflux of fluoroquinolones coupled with a relaxed DNA supercoiling state that buffers cells against GyrAB inhibition by fluoroquinolones.

scholarly journals Cellular ATP Levels Determine the Stability of a Nucleotide Kinase

2021 ◽  
Vol 8 ◽  
Author(s):  
Oliver Brylski ◽  
Puja Shrestha ◽  
Patricia Gnutt ◽  
David Gnutt ◽  
Jonathan Wolf Mueller ◽  
...  
Keyword(s):  
Protein Stability ◽  
Bound States ◽  
Atp Depletion ◽  
Aps Kinase ◽  
Cellular Processes ◽  
Atp Levels ◽  
Stability Change ◽  
Cell Stability ◽  
The Stability ◽  
Nucleotide Kinase

The energy currency of the cell ATP, is used by kinases to drive key cellular processes. However, the connection of cellular ATP abundance and protein stability is still under investigation. Using Fast Relaxation Imaging paired with alanine scanning and ATP depletion experiments, we study the nucleotide kinase (APSK) domain of 3′-phosphoadenosine-5′-phosphosulfate (PAPS) synthase, a marginally stable protein. Here, we show that the in-cell stability of the APSK is determined by ligand binding and directly connected to cellular ATP levels. The observed protein stability change for different ligand-bound states or under ATP-depleted conditions ranges from ΔGf0 = -10.7 to +13.8 kJ/mol, which is remarkable since it exceeds changes measured previously, for example upon osmotic pressure, cellular stress or differentiation. The results have implications for protein stability during the catalytic cycle of APS kinase and suggest that the cellular ATP level functions as a global regulator of kinase activity.

scholarly journals Analysis of stochastic timing of intracellular events with gene switching

2019 ◽  
Author(s):  
Khem Raj Ghusinga ◽  
Abhyudai Singh
Keyword(s):  
First Passage Time ◽  
Regulatory Protein ◽  
Gene Activation ◽  
Threshold Level ◽  
Passage Time ◽  
First Passage ◽  
Cellular Processes ◽  
Event Timing ◽  
Activation Rates ◽  
Gene Switching

AbstractAn important step in execution of several cellular processes is accumulation of a regulatory protein up to a specific threshold level. Since production of a protein is inherently stochastic, the time at which its level crosses a threshold exhibits cell-to-cell variation. A problem of interest is to characterize how the statistics of event timing is affected by various steps of protein expression. Our previous work studied this problem by considering a gene expression model where gene was always active. Here we extend our analysis to a scenario where gene stochastically switches between active and inactive states. We formulate event timing as the first-passage time for a protein’s level to cross a threshold and investigate how the rates of gene activation/inactivation affect the distribution and moments of the first-passage time. Our results show that both the time-scale of gene switching with respect to the protein degradation rate as well as the ratio of the gene inactivation to gene activation rates are important parameters in shaping the event-timing distribution.

scholarly journals Developmentally regulated GTPases: structure, function and roles in disease

2021 ◽  
Author(s):  
Christian A. E. Westrip ◽  
Qinqin Zhuang ◽  
Charlotte Hall ◽  
Charlotte D. Eaton ◽  
Mathew L. Coleman
Keyword(s):  
Cell Proliferation ◽  
Structural Biology ◽  
Regulatory Protein ◽  
Growth Control ◽  
Developmentally Regulated ◽  
Binding Partner ◽  
Cellular Processes ◽  
Gtp Binding ◽  
Evolutionarily Conserved ◽  
Cell Growth Control

AbstractGTPases are a large superfamily of evolutionarily conserved proteins involved in a variety of fundamental cellular processes. The developmentally regulated GTP-binding protein (DRG) subfamily of GTPases consists of two highly conserved paralogs, DRG1 and DRG2, both of which have been implicated in the regulation of cell proliferation, translation and microtubules. Furthermore, DRG1 and 2 proteins both have a conserved binding partner, DRG family regulatory protein 1 and 2 (DFRP1 and DFRP2), respectively, that prevents them from being degraded. Similar to DRGs, the DFRP proteins have also been studied in the context of cell growth control and translation. Despite these proteins having been implicated in several fundamental cellular processes they remain relatively poorly characterized, however. In this review, we provide an overview of the structural biology and biochemistry of DRG GTPases and discuss current understanding of DRGs and DFRPs in normal physiology, as well as their emerging roles in diseases such as cancer.

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