Probing the Interfacial Peptides/Proteins by Using Sum Frequency Generation Spectroscopy with Hamiltonian Approach Data Analysis Method
Creators: name: Lu, Tieyi
Publisher: name: My University
Year: 2022
Subjects: subject: Sum Frequency Generation vibrational spectroscopy
subject: Interfacial proteins/peptides
subject: Hamiltonian local mode approximation method
subject: MD Simulation
subject: Chemistry
subject: Science

description: Interfacial protein behavior has been extensively studied due to its tremendous impact on many biological applications and related research fields, such as biosensors, protein-resistant anti-fouling coatings, protein-drug formulations, biomedical implants, etc. However, it is still challenging to probe the interfacial protein behavior at buried solid/liquid interface in situ in real time. Many traditional analytical tools that are surface-sensitive require high vacuum to operate, which cannot be applied to study solid/liquid interfaces. Sum Frequency Generation (SFG) vibrational spectroscopy has been developed into a powerful tool to characterize the interfacial protein molecules due to its sub-monolayer surface sensitivity and in situ detecting capability without the need for high vacuum. Besides, some detailed structural information (e.g., the orientation or tilt and twist angles) of the interfacial protein molecules can also be elucidated by interpreting SFG spectra, which is difficult to access with other analytical tools. This thesis research focuses on the development and application of a systematic method to deduce interfacial peptide and protein structures using SFG spectroscopy. Particularly, this research adopted Hamiltonian local mode approximation method to calculate SFG spectra as a function of the interfacial peptide/protein orientation based on the input peptide/protein conformation. This newly developed method that combines SFG technique and Hamiltonian analysis method can evaluate the orientation and conformation of interfacial proteins by comparing the matching scores between calculated orientation dependent SFG spectra of different input conformations and experimental SFG spectra. Such a method was successfully applied to study molecular structures of a variety of peptides/proteins at buried interfaces in situ. This method makes it possible to monitor the time-dependent behavior of proteins during adsorption, understand the protein aggregation mechanism on surfaces, investigate the anti-fouling process, and optimize antibody drug formulation, etc. This method broadens the application of SFG technique in the biological research field and adds a new toolset for studying the detailed molecular structural information of biomolecules at the solid/liquid interface. The thesis is presented as follows: Chapter 1 briefly introduces the background of the thesis research and the SFG technique. Chapter 2 discusses the details of the Hamiltonian approach developed for SFG spectra calculation and methods for protein structural determination using SFG. Chapters 3, 4, and 5 presents the applications of the Hamiltonian analysis method combined with SFG data on solving the molecular interfacial structures of adsorbed proteins including bovine serum protein, fibrinogen, and antibody drugs respectively. Chapter 6 elucidates the interfacial structures of barnacle peptides to understand biofouling mechanisms using SFG experiments, molecular dynamics simulations, and Hamiltonian spectral calculations. Chapter 7 summarizes the main findings in this thesis research and proposes some future directions. This research develops a widely applicable approach to use SFG to characterize molecular structures of peptides and proteins at buried interfaces in situ.