Yue Ren

Date of Graduation


Document Type


Degree Type



Eberly College of Arts and Sciences



Committee Chair

Blake Mertz

Committee Co-Chair

Justin Legleiter

Committee Member

Stephen Valentine


Peptides with the ability to bind and insert into the cell membrane are an ever-growing field of research due to their potential biomedical applications. pH (Low) Insertion Peptide (pHLIP), which is a water-soluble polypeptide derived from helix C of bacteriorhodopsin, has the ability to insert into a membrane at acidic pH to form a stable transmembrane alpha-helix. The insertion process takes place in three stages: pHLIP is unstructured and soluble in water at neutral pH (state I), unstructured and bound to the surface of a membrane at neutral pH (state II), and inserted into the membrane as an alpha-helix at low pH (state III). It has been shown that pHLIP binding and insertion occurs over large timescales and multiple kinetic steps from state I to state III. Our study focuses on the initial step, uncoiled pHLIP binding to a lipid bilayer surface, using enhanced sampling molecular dynamics simulation techniques. We have quantified the thermodynamics of this process by computing the free energy change upon binding of a pHLIP variant at several orientations to model lipid bilayers. In addition, our studies provide atomistic details about the binding behaviors of pHLIP to a lipid bilayer that provide a fundamental understanding of the biophysical underpinnings of the pHLIP mechanism.