(681d) Ipro+/- Computational Protein Design Tool for Predicting Indels Along with Substitutions for Redesign of Channel Proteins and Enzymes Alike

Authors: 
Chowdhury, R. - Presenter, The Pennsylvania State University
Maranas, C., The Pennsylvania State University
v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);}

Kevin RATUL CHOWDHURY 2 1 2019-02-13T01:38:00Z 2019-04-12T17:11:00Z 2019-04-12T17:11:00Z 1 443 2530 21 5 2968 16.00

Clean Clean false false false false EN-US X-NONE X-NONE


/* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri",sans-serif; mso-bidi-font-family:"Times New Roman";}


text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">POREDESIGNER: A COMPUTATIONAL TOOL FOR THE DESIGN OF MEMBRANE
PORES FOR SEPARATIONS

text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">

text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">Ratul
Chowdhury, Department of Chemical Engineering. The Pennsylvania State
University, University Park, Pennsylvania 16802, United States

text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">ratul@psu.edu

text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">Manish
Kumar, Department of Chemical Engineering. The Pennsylvania State University

text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">Costas
D Maranas, Department of Chemical Engineering. The
Pennsylvania State University

text-align:center;line-height:normal;mso-layout-grid-align:none;text-autospace:
none">

normal;mso-layout-grid-align:none;text-autospace:none"> 10.0pt;font-family:" arial>

normal;mso-layout-grid-align:none;text-autospace:none"> 10.0pt;font-family:" arial>Key Words:       aquaporin, computational protein design, OmpF,
water purification, optimization

normal;mso-layout-grid-align:none;text-autospace:none"> 10.0pt;font-family:" arial>

justify;line-height:normal;mso-layout-grid-align:none;text-autospace:none">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.

justify;line-height:normal;mso-layout-grid-align:none;text-autospace:none">

normal;mso-layout-grid-align:none;text-autospace:none"> " arial new roman line>

normal;mso-layout-grid-align:none;text-autospace:none">

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" stroked="f">

Figure  SEQ Figure \* ARABIC 1. Two mutations from PoreDesigner predicted in silico redesign of OmpF. The D113W and S125W mutations resulted in a smaller pore lumen and a more hydrophobic inner pore wall. The wild type residues have been shown in green and the altered residues have been shown as pink sticks.


 Figure 1. Two mutations from PoreDesigner predicted in silico redesign of OmpF. The D113W and S125W mutations resulted in a smaller pore lumen and a more hydrophobic inner pore wall. The wild type residues have been shown in green and the altered residues have been shown as pink sticks.