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application/pdf http://hdl.handle.net/2142/92708 en Copyright 2016 Javier Baylon Cardiel Membrane Peripheral proteins Molecular dynamics Lipids Atomic-level characterization of protein-lipid interactions using molecular dynamics simulations text text Tajkhorshid, Emad Tajkhorshid, Emad Gennis, Robert B. Rienstra, Chad Schuler, Mary Baylon Cardiel, Javier Lorenzo 2016-11-10T17:49:42Z 2016-11-10T17:49:42Z 2016-06-01 2016-08 Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein–membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics (MD) simulations offer a suitable approach to study protein–lipid interactions with high spatial and temporal resolution. Here, we present a summary of recent applications of MD simulations to study the interaction of different classes of membrane proteins with lipid bilayers at the atomic level. Specific systems studied include membrane-bound cytochrome P450 (CYP) enzymes, a class membrane proteins involved in the metabolism of a wide range of molecules, the hemagglutinin fusion peptide (HAfp), a small peptide that mediates the fusion process of the influenza virus to a host cell, and the T-cell immunoglobulin and mucin domain (Tim) proteins, involved in the mechanism of lipid recognition by T-cells. Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2016-11-09 without embargo terms The student, Javier Baylon Cardiel, accepted the attached license on 2016-05-31 at 11:52. The student, Javier Baylon Cardiel, submitted this Dissertation for approval on 2016-05-31 at 11:59. This Dissertation was approved for publication on 2016-06-01 at 15:22. DSpace SAF Submission Ingestion Package generated from Vireo submission #9633 on 2016-11-09 at 10:20:54 Made available in DSpace on 2016-11-10T17:49:42Z (GMT). No. of bitstreams: 2 BAYLONCARDIEL-DISSERTATION-2016.pdf: 51744367 bytes, checksum: a95cddd47e609b9d7a6ec046bff896be (MD5) LICENSE.txt: 4218 bytes, checksum: 58d6555780e4dc4718df5de93dd5fffc (MD5) Previous issue date: 2016-06-01 School of Molecular & Cell Bio Biophysics & Computnl Biology University of Illinois at Urbana-Champaign Dissertation Ph.D.