3 research outputs found
All-atom molecular dynamics comparison of disease-associated zinc fingers
<p>An important regulatory domain of NF-B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO’s zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To discern structural and dynamical differences between these disease states, we present results of 48-s of molecular dynamics simulations for three zinc finger systems each in two states, with and without zinc-bound and correspondingly appropriate cysteine thiol/thiolate configurations. The wild-type protein, often studied for its role in cancer, maintains the most rigid and conformationally stable zinc-bound configuration compared with the diseased counterparts. The glaucoma-related protein has persistent loss of secondary structure except within the dominant conformation. Conformational overlap between wild-type and glaucoma isoforms indicate a competitive binding mechanism may be substantial in the malfunctioning configuration, while the alpha-helical disruption of the ectodermal dysplasia suggests a loss of binding selectivity is responsible for aberrant function.</p
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
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