Chemical selectivity principles of translocation catalysis by membrane transporters

Membrane transporter proteins act as the gatekeepers of living cells. By passage through transporter proteins and their alternate access mechanism, metabolites and exogenous materials can cross lipid bilayers and travel to cellular destinations. Transporter-mediated translocation reactions pose an interesting question within the realm of chemical biology. Unlike traditional enzymes, transporters do not make or break any substrate bonds. Instead, the transporter undergoes distinct conformational change as the substrate traverses the lipid bilayer. Given how many molecules – including drug chemical structures which have not necessarily coevolved with transporters – can be translocated by the same carrier proteins, the question arises as to how transporter proteins maintain their selectivity. To ascertain selectivity principles for membrane transporter reactions, I have employed large scale molecular dynamics simulations and Markov state models within this dissertation. I detail how substrate scope, surrounding environment, cellular regulation, and sequence evolution may affect transporter selectivity. A cofactor-independent sugar uniporter family, SWEET (Sugars Will Eventually be Exported Transporters), as well as a PIP (plasma membrane intrinsic protein) aquaporin, are used as example systems. I focus on unveiling how the molecular mechanism of AtSWEET13 sugar transporter differentiates between different substrates, and then equip those results to computationally design selective mutants capable of abolishing transport for one sugar but not the other. Fundamental understanding is then developed through the modeling of realistic lipid bilayers. The impact the membrane environment poses onto transport functions is evaluated by using aquaporin SoPIP2;1 as a model. Forms of transporter activity regulation via phosphorylation and oligomerization state are revealed on OsSWEET2b sugar transporter. And experimental and state-of-the-art predictive computational technologies are tested to probe gain-of-function and context-specific mutations using AtSWEET13. At its core, this thesis demonstrates that transporter proteins behave like “physical” enzymes. Transporters possess central binding sites with conserved molecular recognition functions; however, a potential substrate is prepared for transport catalysis by means of discriminatory molecular recognition events prior to alternate access. The fundamental differences in opposing ligand’s transportability can be exacerbated by tuning of the membrane environment, cellular regulation schemes, or mutation to the transporter’s transmembrane channel. Targeting of these latter factors regulating transporter function will prove beneficial to future biotechnology or small molecule development endeavors.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2024

Author dc:creator

• Weigle, Austin Tyler

Contributors dc:contributor

• Shukla, Diwakar
• Gruebele, Martin
• Chen, Li-Qing
• Mitchell, Douglas

• Membrane Transporter
• Molecular Dynamics Simulation
• Adaptive Sampling
• Markov State Models
• Substrate Selectivity
• Lipid Bilayer
• Protein Engineering
• Allostery
• Phosphorylation
• Membrane Protein
• Variant Effect
• Protein-lipid Interactions

Statement dc:rights

• Copyright 2024 Austin Tyler Weigle

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/124619

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F124619