(681d) Ipro+/- Computational Protein Design Tool for Predicting Indels Along with Substitutions for Redesign of Channel Proteins and Enzymes Alike
AIChE Annual Meeting
2019
2019 AIChE Annual Meeting
Food, Pharmaceutical & Bioengineering Division
Computational Approaches to Protein Engineering
Thursday, November 14, 2019 - 1:24pm to 1:42pm
POREDESIGNER: A COMPUTATIONAL TOOL FOR THE DESIGN OF MEMBRANE
PORES FOR SEPARATIONS Ratul
Chowdhury, Department of Chemical Engineering. The Pennsylvania State
University, University Park, Pennsylvania 16802, United States ratul@psu.edu Manish
Kumar, Department of Chemical Engineering. The Pennsylvania State University Costas
D Maranas, Department of Chemical Engineering. The
Pennsylvania State University Key Words: aquaporin, computational protein design, OmpF,
water purification, optimization Monodispersed
angstrom-size pores embedded in a suitable matrix are promising for highly
selective membrane-based separations. They can provide substantial energy
savings in water treatment and small molecule bioseparations.
Such membrane proteins (primarily aquaporins) are commonplace in biological
membranes but difficult to implement in synthetic industrial membranes due to
their modest and non-tunable selectivity. Here we describe PoreDesigner, a
computational design workflow for the redesign of the robust beta-barrel Outer
Membrane Protein F as a scaffold targeting of any specified pore diameter
(spanning 3–10 Å), internal geometry and chemistry. PoreDesigner uses a mixed-integer
linear program to optimally place long side -chain hydrophobic amino acids at
the pore constriction region that yield a smaller and more hydrophobic pore by
maximizing the interaction energy between the pore wall and the permeating
water wire. We appended a design assessment step in each iteration by accepting
only those designs that fit the user-fed pore dimensions. We first ran
PoreDesigner to obtain pore sizes lesser than 4 Å that would exhibit
aquaporin-like single file water transport yet maintaining high water
permeation rates. 40 accepted OmpF redesigns were obtained and were classified
as off-center (OCD), uniform closure (UCD), and cork-screw designs (CSD)
dictated by their internal pore architecture. The narrowest pore design from
each category was chosen and set in a membrane-patch and an all-atom 200ns molecular
dynamics forward-osmosis simulation was performed to corroborate the
PoreDesigner-predicted pore sizes. Subsequently, stopped-flow light scattering
experiments on these three designs revealed complete salt rejection by the UCD
mutant and an order of magnitude higher single-channel water permeabilities
than any reported aquaporin till date (for all three designs). Follow-up
efforts are being made to tune the membrane-pore interactions for various
biomimetic membrane materials, by systematic alteration of the hydrophobicity
of the membrane-facing residues without altering their pore size. This would enable
easier incorporation of these redesigned proteins in 2D planar membrane sheets
and serve as viable filtration assemblies for performing precise angstrom-scale
separations. PoreDesigner has been made freely downloadable from http://www.maranasgroup.com/software.htm.
PORES FOR SEPARATIONS Ratul
Chowdhury, Department of Chemical Engineering. The Pennsylvania State
University, University Park, Pennsylvania 16802, United States ratul@psu.edu Manish
Kumar, Department of Chemical Engineering. The Pennsylvania State University Costas
D Maranas, Department of Chemical Engineering. The
Pennsylvania State University Key Words: aquaporin, computational protein design, OmpF,
water purification, optimization Monodispersed
angstrom-size pores embedded in a suitable matrix are promising for highly
selective membrane-based separations. They can provide substantial energy
savings in water treatment and small molecule bioseparations.
Such membrane proteins (primarily aquaporins) are commonplace in biological
membranes but difficult to implement in synthetic industrial membranes due to
their modest and non-tunable selectivity. Here we describe PoreDesigner, a
computational design workflow for the redesign of the robust beta-barrel Outer
Membrane Protein F as a scaffold targeting of any specified pore diameter
(spanning 3–10 Å), internal geometry and chemistry. PoreDesigner uses a mixed-integer
linear program to optimally place long side -chain hydrophobic amino acids at
the pore constriction region that yield a smaller and more hydrophobic pore by
maximizing the interaction energy between the pore wall and the permeating
water wire. We appended a design assessment step in each iteration by accepting
only those designs that fit the user-fed pore dimensions. We first ran
PoreDesigner to obtain pore sizes lesser than 4 Å that would exhibit
aquaporin-like single file water transport yet maintaining high water
permeation rates. 40 accepted OmpF redesigns were obtained and were classified
as off-center (OCD), uniform closure (UCD), and cork-screw designs (CSD)
dictated by their internal pore architecture. The narrowest pore design from
each category was chosen and set in a membrane-patch and an all-atom 200ns molecular
dynamics forward-osmosis simulation was performed to corroborate the
PoreDesigner-predicted pore sizes. Subsequently, stopped-flow light scattering
experiments on these three designs revealed complete salt rejection by the UCD
mutant and an order of magnitude higher single-channel water permeabilities
than any reported aquaporin till date (for all three designs). Follow-up
efforts are being made to tune the membrane-pore interactions for various
biomimetic membrane materials, by systematic alteration of the hydrophobicity
of the membrane-facing residues without altering their pore size. This would enable
easier incorporation of these redesigned proteins in 2D planar membrane sheets
and serve as viable filtration assemblies for performing precise angstrom-scale
separations. PoreDesigner has been made freely downloadable from http://www.maranasgroup.com/software.htm.