5 research outputs found
Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning
<p>Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associated single deletion of LYS9 in the light chain. By combining supervised and unsupervised machine learning methodologies and more traditional structural analyses on data from 10 μs molecular dynamics simulations, we show that the conformational ensemble of the ΔK9 mutant is significantly perturbed. Our analyses consistently indicate that LYS9 deletion destabilizes both the catalytic cleft and regulatory functional regions and result in some conformational changes that occur in tens to hundreds of nanosecond scaled motions. We also reveal that the two forms of thrombin each prefer a distinct binding mode of a Na<sup>+</sup> ion. We expand our understanding of previous experimental observations and shed light on the mechanisms of the LYS9 deletion associated bleeding disorder by providing consistent but more quantitative and detailed structural analyses than early studies in literature. With a novel application of supervised learning, i.e. the decision tree learning on the hydrogen bonding features in the wild-type and ΔK9 mutant forms of thrombin, we predict that seven pairs of critical hydrogen bonding interactions are significant for establishing distinct behaviors of wild-type thrombin and its ΔK9 mutant form. Our calculations indicate the LYS9 in the light chain has both localized and long-range allosteric effects on thrombin, supporting the opinion that light chain has an important role as an allosteric effector.</p
All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10
Advancing the use of therapeutic
nucleic acids requires understanding
the chemical and structural properties that allow these polymers to
promote the death of malignant cells. Here we explore Zn<sup>2+</sup> complexation by the fluoropyrimidine polymer F10, which has strong
activities in multiple preclinical models of cancer. Delivery of fluoropyrimidine
FdUMP in the 10-residue polymer F10 rather than the nucleobase (5-fluorouracil)
allows consideration of metal ion binding effects on drug delivery.
The differences in metal ion interactions with fluoropyrimidine compared
to normal DNA results in conformation changes that affect protein
binding, cell uptake, and codelivery of metals such as zinc, and the
cytoxicity thereof. Microsecond-time-scale, all-atom simulations of
F10 predict that zinc selectively stabilizes the polymer via interactions
with backbone phosphate groups and suggest a mechanism of complexation
for the zinc-base interactions shown in previous experimental work.
The positive zinc ions are attracted to the negatively charged phosphate
groups. Once the Zn<sup>2+</sup> ions are near F10, they cause the
base’s N3 nitrogen to deprotonate. Subsequently, magnesium
atoms displace zinc from their interactions with phosphate, freeing
the zinc ions to interact with the FdU bases by forming weak interactions
with the O4 oxygen and the fluorine attached to C5. These interactions
of magnesium with phosphate groups and zinc with nucleobases agree
with previous experimental results and are seen in MD simulations
only when magnesium is introduced after N3 deprotonation, indicating
a specific order of metal binding events. Additionally, we predict
interactions between zinc and F10’s O2 atoms, which were not
previously observed. By comparison to 10mers of polyU and polydT,
we also predict that the presence of fluorine increases the binding
affinity of zinc to F10 relative to analogous strands of RNA and DNA
consisting of only native nucleotides
All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic
Given
their increasingly frequent usage, understanding the chemical
and structural properties which allow therapeutic nucleic acids to
promote the death of cancer cells is critical for medical advancement.
One molecule of interest is a 10-mer of FdUMP (5-fluoro-2′-deoxyuridine-5′-O-monophosphate)
also called F10. To investigate causes of structural stability, we
have computationally restored the 2′ oxygen on each ribose
sugar of the phosphodiester backbone, creating FUMP[10]. Microsecond
time-scale, all-atom, simulations of FUMP[10] in the presence of 150
mM MgCl<sub>2</sub> predict that the strand has a 45% probability
of folding into a stable hairpin-like secondary structure. Analysis
of 16 μs of data reveals phosphate interactions as likely contributors
to the stability of this folded state. Comparison with polydT and
polyU simulations predicts that FUMP[10]’s lowest order structures
last for one to 2 orders of magnitude longer than similar nucleic
acid strands. Here we provide a brief structural and conformational
analysis of the predicted structures of FUMP[10], and suggest insights
into its stability via comparison to F10, polydT, and polyU
Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator)
Zinc-finger
proteins are regulators of critical signaling pathways
for various cellular functions, including apoptosis and oncogenesis.
Here, we investigate how binding site protonation states and zinc
coordination influence protein structure, dynamics, and ultimately
function, as these pivotal regulatory proteins are increasingly important
for protein engineering and therapeutic discovery. To better understand
the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB
essential modulator), as well as the role of zinc, we present results
of 20 μs molecular dynamics trajectories, 5 μs for each
of four active site configurations. Consistent with experimental evidence,
the zinc ion is essential for mechanical stabilization of the functional,
folded conformation. Hydrogen bond motifs are unique for deprotonated
configurations yet overlap in protonated cases. Correlated motions
and principal component analysis corroborate the similarity of the
protonated configurations and highlight unique relationships of the
zinc-bound configuration. We hypothesize a potential mechanism for
zinc binding from results of the thiol configurations. The deprotonated,
zinc-bound configuration alone predominantly maintains its tertiary
structure throughout all 5 μs and alludes rare conformations
potentially important for (im)Âproper zinc-finger-related protein–protein
or protein–DNA interactions