Research & Publications

Graduate Research at University of Pennsylvania

• Computational Protein Design (2 projects • 18 designed proteins • 16 confirmed to fold correctly)

  1. Designed a wide variation of charges for a short peptide of 29 amino acid residues (~3600 Da).
     • 17 peptide sequences calculated, each with distinguished charges from -8, -7, -6, …, +6, +7, +8 (17 charge states).
     • 15 of the 17 sequences folded as desired (88% success rate).
     • 13 of the 18 exterior residues (72%) in the peptide were modified without disturbing the folded structures.
  2. Designed a super-positive variant of human carbonic anhydrase II enzyme with net charge of +21 (natural enzyme has -1 charge).
     • This is the first example of a computationally designed super-positively charged enzyme.
     • 20 out of the enzyme’s 70 exterior residues (28%) were mutated, without compromising the enzyme’s folded structure or eliminating functionality (81% activity retained).
     • The super-positive enzyme variant can be directly encapsulated within a ferritin cage (negatively charged), without adding a super-positively charged fusion partner (previous encapsulation method).
     • Encapsulation leads to enhanced thermal stability and activity (63% enhanced at 40 °C).

• Molecular dynamics (MD) simulations (uncovering unstable interactions in problematic sequences.)

  • For sequences that did not fold correctly in synthesis, MD Simulations revealed unstable sidechain interactions near the peptides’ N-terminus. MD supported redesigns which eliminated the found interactions folded correctly in experiments.

Publications