scholarly journals Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability

2020 ◽  
Vol 22 (1) ◽  
pp. 76
Author(s):  
Aaron Morgan ◽  
Sarah LeGresley ◽  
Christopher Fischer
Keyword(s):  
Free Energy ◽  
Dna Replication ◽  
Recent Work ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Genetic Information ◽  
Molecular Machines ◽  
Mechanical Work ◽  
Eukaryotic Genome ◽  
Hydrolysis Of

The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.

Initiation of archaeal DNA replication

2003 ◽  
Vol 31 (3) ◽  
pp. 669-673 ◽  
Author(s):  
E.R. Jenkinson ◽  
J.P.J. Chong
Keyword(s):  
Dna Replication ◽  
Recent Work ◽  
Genetic Information ◽  
Genetic Material ◽  
50Th Anniversary ◽  
Enormous Amount ◽  
Biological Concepts ◽  
Archaeal Dna Replication ◽  
The Way

The identification of DNA as the genetic material and the elucidation of its structure by Watson and Crick [Watson and Crick, (1953) Nature (London) 171, 737–738], which has its 50th anniversary this year, first suggested the simple elegance with which the problem of passing on precise genetic information from one generation to the next could be solved. Semi-conservative replication is perhaps one of the simplest biological concepts to explain and understand. However, despite an enormous amount of effort in the intervening years, details of the way in which this process is regulated and performed are still unclear in many organisms. Recent work suggests that, due to their simplicity, the Archaea may make a good model for understanding some of the aspects of eukaryotic replication that still elude us.

PrimPol (Primase/Polymerase), replicating enzyme – A mini review

2020 ◽  
Vol 2 (4) ◽  
pp. 89-92
Author(s):  
Muhammad Amir ◽  
Sabeera Afzal ◽  
Alia Ishaq
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Genetic Information ◽  
Nuclear Dna ◽  
De Novo ◽  
Dna Polymerases ◽  
Test Site ◽  
Mitochondrial Dna Replication ◽  
Dna Template ◽  
Preliminary Phase

Polymerases were revealed first in 1970s. Most important to the modest perception the enzyme responsible for nuclear DNA replication that was pol , for DNA repair pol and for mitochondrial DNA replication pol  DNA construction and renovation done by DNA polymerases, so directing both the constancy and discrepancy of genetic information. Replication of genome initiate with DNA template-dependent fusion of small primers of RNA. This preliminary phase in replication of DNA demarcated as de novo primer synthesis which is catalyzed by specified polymerases known as primases. Sixteen diverse DNA-synthesizing enzymes about human perspective are devoted to replication, reparation, mutilation lenience, and inconsistency of nuclear DNA. But in dissimilarity, merely one DNA polymerase has been called in mitochondria. It has been suggest that PrimPol is extremely acting the roles by re-priming DNA replication in mitochondria to permit an effective and appropriate way replication to be accomplished. Investigations from a numeral of test site have significantly amplified our appreciative of the role, recruitment and regulation of the enzyme during DNA replication. Though, we are simply just start to increase in value the versatile roles that play PrimPol in eukaryote.

DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide

2018 ◽  
Vol 17 (08) ◽  
pp. 1850050 ◽  
Author(s):  
Qiuhan Luo ◽  
Gang Li ◽  
Junping Xiao ◽  
Chunhui Yin ◽  
Yahui He ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecule ◽  
Carbonyl Group ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Metsulfuron Methyl ◽  
Catalytic Role ◽  
Hydrolysis Of

Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.

scholarly journals The Free Energy of Hydrolysis of Adenosine to Inosine and Ammonia

1967 ◽  
Vol 242 (20) ◽  
pp. 4711-4714 ◽  
Author(s):  
Richard Wolfenden
Keyword(s):  
Free Energy ◽  
Hydrolysis Of

scholarly journals Use of scaled-particle theory in the assessment of the Ph4As+/Ph4B− assumption for single ions

1979 ◽  
Vol 57 (1) ◽  
pp. 71-76 ◽  
Author(s):  
Michael H. Abraham ◽  
Asadollah Nasehzadeh
Keyword(s):  
Free Energy ◽  
Recent Work ◽  
Scaled Particle Theory ◽  
Cavity Formation ◽  
Energy Term ◽  
Free Energies ◽  
Particle Theory ◽  
Novel Method ◽  
Energy Of Interaction ◽  
Solvent Molecules

A novel method for the assessment of the Ph4As+/Ph4B− assumption for free energies of transfer of single ions has recently been suggested by Treiner, and used by him to deduce that the assumption is not valid for transfers between water, propylene carbonate, sulpholane, dimethylsulphoxide, N-methyl-2-pyrrolidone, and perhaps also dimethylformamide. The basis of the method is the estimation of the free energy of cavity formation by scaled-particle theory, together with the hypothesis that the free energy of interaction of Ph4As+ (or Ph4B−) with solvent molecules is the same in all solvents, ΔGt0(int) = 0. It is shown in the present paper that (a) whether or not the Ph4As+/Ph4B− assumption applies to transfer to a given solvent depends on which other solvent is taken as the reference solvent in Treiner's method, (b) the calculation of the cavity free energy term by scaled-particle theory and by the theory of Sinanoglu – Reisse – Moura Ramos (SRMR) yields values so different that the method cannot be considered reliable, (c) the calculation of cavity enthalpies and entropies for Ph4As+ or Ph4B− by scaled-particle theory yields results that are chemically not reasonable, (d) the hypothesis that ΔGt0(int) = 0 conflicts with SRMR theory, and (e) the conclusions reached by Treiner are not in accord with recent work that in general supports the Ph4As+/Ph4B− assumption for solvents that are rejected by Treiner.

Linear Free Energy Relationships in the Intrinsic and GTPase Activating Protein-Stimulated Guanosine 5‘-Triphosphate Hydrolysis of p21ras†

Biochemistry ◽  
1996 ◽  
Vol 35 (45) ◽  
pp. 14225-14231 ◽  
Author(s):  
T. Schweins ◽  
M. Geyer ◽  
H. R. Kalbitzer ◽  
A. Wittinghofer ◽  
A. Warshel
Keyword(s):  
Free Energy ◽  
Linear Free Energy Relationships ◽  
Gtpase Activating Protein ◽  
Linear Free Energy ◽  
Energy Relationships ◽  
Hydrolysis Of

Heat capacity of activation for the hydrolysis of methanesulfonyl chloride and benzenesulfonyl chloride in light and heavy water

1969 ◽  
Vol 47 (22) ◽  
pp. 4199-4206 ◽  
Author(s):  
R. E. Robertson ◽  
B. Rossall ◽  
S. E. Sugamori ◽  
L. Treindl
Keyword(s):  
Heat Capacity ◽  
Free Energy ◽  
Temperature Dependence ◽  
Heavy Water ◽  
Bond Formation ◽  
Sulfonyl Chlorides ◽  
Benzenesulfonyl Chloride ◽  
Methanesulfonyl Chloride ◽  
Hydrolysis Of ◽  
Parameter Temperature Dependence

Rates of solvolysis of methanesulfonyl chloride and benzenesulfonyl chloride have been determined in H2O and D2O. The free energy, enthalpy, entropy, and heat capacity of activation were calculated. The exceptional accuracy of the data permitted an estimation of dΔCp≠/dT from a four parameter temperature dependence of the kinetic rates.From these data we conclude that both sulfonyl chlorides hydrolyse by the same mechanism (Sn2) The change in R from CH3 to C6H5 in RSO2Cl did not alter ΔCp≠ but ΔS≠ (20°) was changed from −8.32 to −13.25 cal deg−1 mole−1, respectively. The significance of this difference is attributed to the probability of bond formation rather than to differences in solvent reorganization.

scholarly journals Archaeal Orc1 protein interacts with T-rich single-stranded DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Katarzyna Wegrzyn ◽  
Igor Konieczny
Keyword(s):  
Dna Replication ◽  
Replication Initiation ◽  
Single Stranded Dna ◽  
Dna Replication Initiation ◽  
Double Stranded Dna ◽  
Nucleoprotein Complexes ◽  
Eukaryotic Organisms ◽  
Replication Initiation Proteins ◽  
Hydrolysis Of ◽  
Replication Activity

Abstract Objective The ability to form nucleoprotein complexes is a fundamental activity of DNA replication initiation proteins. They bind within or nearby the region of replication origin what results in melting of a double-stranded DNA (dsDNA) and formation of single-stranded DNA (ssDNA) region where the replication machinery can assemble. For prokaryotic initiators it was shown that they interact with the formed ssDNA and that this interaction is required for the replication activity. The ability to interact with ssDNA was also shown for Saccharomyces cerevisiae replication initiation protein complex ORC. For Archaea, which combine features of both prokaryotic and eukaryotic organisms, there was no evidence whether DNA replication initiators can interact with ssDNA. We address this issue in this study. Results Using purified Orc1 protein from Aeropyrum pernix (ApOrc1) we analyzed its ability to interact with ssDNA containing sequence of an AT-rich region of the A. pernix origin Ori1 as well as with homopolymers of thymidine (polyT) and adenosine (polyA). The Bio-layer interferometry, surface plasmon resonance and microscale thermophoresis showed that the ApOrc1 can interact with ssDNA and it binds preferentially to T-rich ssDNA. The hydrolysis of ATP is not required for this interaction.

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