Regensburg 2019 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 12: Poster II
BP 12.31: Poster
Dienstag, 2. April 2019, 14:00–16:00, Poster B2
Generalized Markov State Modeling of Electric Field Induced Conformational Changes in the HIV-1 V3 Loop Peptide — Bernhard Reuter1,2, •Daungruthai Jarukanont2, Sina Zendehroud2, and Martin E. Garcia2 — 1Zuse Institute Berlin (ZIB), Berlin, Germany — 2University of Kassel, Kassel, Germany
Conformational changes regulate the physiological functionality of proteins. The influence of environmental conditions on the function and, therefore, on the conformation of proteins is being studied very intensively. In this work, we investigate the influence of a static external electric field on the secondary and tertiary structure formation of the V3 loop of the HIV-1 envelope glycoprotein gp120. Based on extensive molecular dynamics (MD) simulations, the conformational dynamics of the system were modeled applying a recently developed generalized Markov state modeling method termed Generalized Perron Cluster Cluster Analysis (G-PCCA) from [Reuter et al. (2018). JCTC, 14(7), 3579-3594. https://doi.org/10.1021/acs.jctc.8b00079]. G-PCCA enables the unsupervised and automatic coarse graining of both reversible and nonreversible molecular kinetics. Using G-PCCA the dominant conformational dynamics of the system were learned for different strengths of the electric field.