|Institution:||University of Illinois – Urbana-Champaign|
|Keywords:||Molecular Dynamics; Membrane Interface; Lignocellulosic Interface|
|Full text PDF:||http://hdl.handle.net/2142/90518|
Molecular dynamics (MD) has a long history of being used to advance our understanding of the natural world, and is a powerful tool to guide experiments by unraveling the fine details of individual interactions and how these interactions drive dynamics. For molecular events that occur at biological interfaces, MD is unique in being able to simultaneously probe small spatial and temporal scales. This unparalleled resolution offers unique insight to the specific interactions that govern interfacial processes. In the context of this dissertation, MD is applied to processes in membrane biology and biofuel research. Through the use of the Highly Mobile Membrane Mimetic (HMMM) to accelerate phospholipid motion, we show that phospholipid tails insert significantly faster than they do in a conventional bilayer, and repeated insertion of the peripheral membrane protein α-synuclein shows larger conformational variability in the HMMM than was observed in conventional bilayers. Separately, simulations of C2 domain binding of synaptogamin (Syt) to the HMMM demonstrate clear differences in the binding properties between Syt isoforms, and explain the atomic origins of the observed differential kinetics between Syt-1 and Syt-7. Development of the HMMM to extend its applicability to transmembrane systems is also discussed. Transmembrane systems in conventional bilayers are also presented. In conjunction with the parameterization of ubiquinone, its binding and dynamics are reported in both the QA and QB sites of the photosynthetic reaction center of Rhodobacter sphaeroides and the quinone-binding site of ubiquinol oxidase. Recent structural work on the polyaromatic cation transporter EmrE, and its electrostatic locking mechanism governing conformational change, are also discussed. Interactions at the interface of cellulose have also been simulated. The impact of lytic polysaccharide monooxygenase (LPMO) action on cellulose structure and potential product inhibition of cellulose degrading enzymes by oxidized cellulose were monitored while on practicum at the National Renewable Energy Laboratory. Similarly, the mechanism of how lignin interferes with cellulose degradation by cellulases was determined by a multimillion atom simulation analyzed while on practicum at Oak Ridge National Laboratory. Advisors/Committee Members: Tajkhorshid, Emad (advisor), Tajkhorshid, Emad (Committee Chair), Aksimentiev, Aleksei (committee member), Kraft, Mary L (committee member), Crofts, Antony R (committee member).