6 research outputs found
Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods
Hydrogen bonds play a critical role in the folding and
stability
of proteins, such as proteins and nucleic acids, by providing strong
and directional interactions. They help to maintain the secondary
and 3D structure of proteins, and structural changes in these molecules
often result from the formation or breaking of hydrogen bonds. To
gain insights into these hydrogen bonding networks, we applied two
machine learning models - a logistic regression model and a decision
tree model - to study four variants of thrombin: wild-type, ΔK9,
E8K, and R4A. Our results showed that both models have their unique
advantages. The logistic regression model highlighted potential key
residues (GLU295) in thrombin’s allosteric pathways, while
the decision tree model identified important hydrogen bonding motifs.
This information can aid in understanding the mechanisms of folding
in proteins and has potential applications in drug design and other
therapies. The use of these two models highlights their usefulness
in studying hydrogen bonding networks in proteins
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 ÎĽs 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-ÎşB 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-ÎşB
essential modulator), as well as the role of zinc, we present results
of 20 ÎĽs molecular dynamics trajectories, 5 ÎĽs 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 ÎĽs and alludes rare conformations
potentially important for (im)Âproper zinc-finger-related protein–protein
or protein–DNA interactions
Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge
As
the length of molecular dynamics (MD) trajectories grows with
increasing computational power, so does the importance of clustering
methods for partitioning trajectories into conformational bins. Of
the methods available, the vast majority require users to either have
some <i>a priori</i> knowledge about the system to be clustered
or to tune clustering parameters through trial and error. Here we
present non-parametric uses of two modern clustering techniques suitable
for first-pass investigation of an MD trajectory. Being non-parametric,
these methods require neither prior knowledge nor parameter tuning.
The first method, HDBSCAN, is fastî—¸relative to other popular
clustering methodsî—¸and is able to group unstructured or intrinsically
disordered systems (such as intrinsically disordered proteins, or
IDPs) into bins that represent global conformational shifts. HDBSCAN
is also useful for determining the overall stability of a systemî—¸as
it tends to group stable systems into one or two binsî—¸and identifying
transition events between metastable states. The second method, iMWK-Means,
with explicit rescaling followed by K-Means, while slower than HDBSCAN,
performs well with stable, structured systems such as folded proteins
and is able to identify higher resolution details such as changes
in relative position of secondary structural elements. Used in conjunction,
these clustering methods allow a user to discern quickly and without
prior knowledge the stability of a simulated system and identify both
local and global conformational changes
Site-Specific DNA–Doxorubicin Conjugates Display Enhanced Cytotoxicity to Breast Cancer Cells
Doxorubicin (Dox) is widely used
for breast cancer treatment but
causes serious side effects including cardiotoxicity that may adversely
impact patient lifespan even if treatment is successful. Herein, we
describe selective conjugation of Dox to a single site in a DNA hairpin
resulting in a highly stable complex that enables Dox to be used more
effectively. Selective conjugation of Dox to G15 in the hairpin loop
was verified using site-specific labeling with [2-<sup>15</sup>N]-2′-deoxyguanosine
in conjunction with [<sup>1</sup>H–<sup>15</sup>N] 2D NMR,
while 1:1 stoichiometry for the conjugate was validated by ESI-QTOF
mass spectrometry and UV spectroscopy. Molecular modeling indicated
covalently bound Dox also intercalated into the stem of the hairpin
and stability studies demonstrated the resulting Dox-conjugated hairpin
(DCH) complex had a half-life >30 h, considerably longer than alternative
covalent and noncovalent complexes. Secondary conjugation of DCH with
folic acid (FA) resulted in increased internalization into breast
cancer cells. The dual conjugate, DCH-FA, can be used for safer and
more effective chemotherapy with Dox and this conjugation strategy
can be expanded to include additional anticancer drugs