mu ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
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Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...
DNA is a long polymer with the form of a double helix of about two nanometers diameter (2.10-9 meters). It is composed of nucleotides whose sequence carries the information of heredity. The four possible nucleotides have slightly different geometries, and ...
Limited searching in the conformational space is one of the major obstacles for investigating protein dynamics by numerical approaches. For this reason, classical all-atom mol. dynamics (MD) simulations of proteins tend to be confined to local energy min., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In the work presented here, we have focused on mapping mRNA 3' ...
Chloroethenes, and most particularly tetra- (PCE) and trichloroethene (TCE) are major groundwater pollutants due to their extensive industrial use as solvents since the 1920s. The strong electronegativity of the chlorines renders them very stable under aer ...
Macrophage migration inhibitory factor (MIF) is a multifunctional protein and a major mediator of innate immunity. Although X-ray crystallography revealed that MIF exists as a homotrimer, its oligomerization state in vivo and the factors governing its olig ...
Extensive conformational analysis of a series of beta-alkyl substituted cyclopeptides-cyclo(Pro(1)-Xaa(2)-Nle(3)-Ala(4)-Nle(5)-Pro(6) Xaa(7)-Nle(8)-Ala(9)-Nle(10)) and cyclo[Pro(1)-Xaa(2)-Nle(3)-(Cys(4)-Nle(5)-Pro(6)-Xaa(7)-Nle(8)-Cys(9))-N le(10)] as well ...
The soln. structure of the duplex formed by self-pairing of the p-RNA octamer b-D-ribopyranosyl-(2'->4')-(CGAATTCG) was studied by NMR techniques and, independently, by mol.-dynamics calcns. The resonances of all non-exchanging protons, H-bearing C-atoms, ...
The 5'-terminal sequence in the DNA of the parvovirus minute virus of mice (MVM) is a palindrome. It can form a hairpin, the stem of which is entirely base-paired except for three consecutive unpaired nucleotides which form a bubble. Since this structure i ...
We study the behavior of single-stranded DNA (ssDNA) in the presence of well-known drugs with either an intercalating binding mode, such as daunorubicin, actinomycin D, and chloroquine, or a minor groove binding mode, such as netropsin and berenil, by atom ...