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Bioinformatics, Computational and Systems Biology

Bioinformatics, Computational and Systems Biology - Poster Session B

Poster A1 - Comparing the Pore Architecture of Claudin Pores

Thursday, October 24, 2024

2:45 PM - 3:45 PM EST

Location: Exhibit Hall E, F & G

Presenting Author(s)

Alem Yirefu

Undergraduate researcher
Syracuse University
Syracuse, New York, United States

Primary Investigator(s)

Shikha Nangia, PhD (she/her/hers)

Professor and Chair, Biomedical and Chemical Engineering
Syracuse Univeristy
Syracuse, New York, United States

Introduction: Tight junctions are physical barriers composed of multiple transmembrane proteins that
regulate the passage of substances across the paracellular space in epithelial and
endothelial cells. Tight junctions serve various essential functions. In the skin, tight junctions
serve to form a barrier between internal organs and the environment; gut tight junctions are
selectively permeable to allow for the passage of substances such as nutrients; the blood-
brain barrier tight junctions serve to prevent blood-borne toxins from entering the central
nervous system. To fulfill these varying functions, the permeability of tight junctions differs
across various tissues. The passage of substances across the paracellular pathway is size
and charge-selective and depends on the proteins that make up the tight junctions.
Among the proteins that make up tight junctions is the claudin family of proteins, composed
of 27 proteins. Claudins self-assemble via lateral (cis) interactions to form contiguous
strands. The trans (head-on) interaction of these strands with neighboring strands forms
barriers and pores that control the transport of molecules across the intercellular space. The
type and charge of amino acid residues lining the pores determine the properties of the
substances allowed to pass through. In addition, the self-assembly of claudins can be
between the same (homo) or different (hetero) claudins. Cis interactions can be homomeric
or heteromeric, and trans interactions can be homotypic or heterotypic. This study examined claudin pores of various compositions and
architectures to understand the factors influencing paracellular transport.

Materials and

Methods: We used all-atom molecular dynamics (MD) simulations to determine the equilibrated
structure of the tight junction pore formed by claudin-5. The simulations were performed at a
physiological temperature of 310 K and 150 nM ionic concentration. We used the Charmm36
force field to model the proteins and TIP3 water for the simulations. The CAVER extension
of PyMOL was used to determine the tight junction pore size. We also determined the
hydropathy of the tight junction pore using a newly developed computational method called
Protocol for Assigning a Residue’s Character on the Hydropathy (PARCH) scale that assigns
a value between 0 and 10 to each amino acid in the protein. To compute the parch values,
the tight junction proteins were solvated in a shell of explicit water molecules, and the
temperature of the system was increased from 300 K to 800 K. Residues that retain the
water are assigned a hydrophilic or higher parch values than the residues that lose water
more readily have lower parch values on the 0-10 scale. The results of the MD and PARCH
calculations were visualized in PyMol.

Results, Conclusions, and Discussions: Results
Our results show that claudin-5 pores are formed when four protomers interact via
homomeric and homotypic interactions. The pores are smaller than one nanometer with an
average radius of 0.42 ± 0.06 nm. In the narrowest region, the pore radius is 0.33 ± 0.03 nm,
consistent with our previous experimental work. We observed that there are small
fluctuations in the pore’s geometry. Additionally, charged amino residues K48 and K65 lie in
the pore's center and are symmetrically arranged to provide bidirectional selectivity in solute
transport. The hydropathy calculations show high parch values for the pore region compared
to the helical membrane-embedded parts of claudin-5.
Discussions
Although isolating intact claudin pores is still elusive, the pore model provided insight into the
selectivity of the tight junctions at the blood-brain barrier interface. This work has been
extended to other claudin pores. We observed that each claudin has a unique molecular
architecture due to differences in amino acid residues lining the pore walls. The differences
in the architectures of claudin pores have been observed to influence their hydropathy.
Conclusions
Our molecular simulations show that the primary sequence of claudin proteins determines
the selectivity of the tight junction pores, especially the pore-lining residues. Evaluating the
pore architecture of claudin-5 has allowed us to understand the molecular origin of the
selectivity of the tight junctions at the blood-brain barrier interface. Further investigation of
pores formed by other claudins has provided a new understanding of the selective transport
mechanisms across the tight junctions in other parts of the body.

Acknowledgements (Optional):