- 20.12.2017 -
S3 Seminar Rebecca Wade
Date: Wednesday December 20 - 11.00
Venue: S3 Seminar Room, Third floor, Physics building, FIM Department
Speaker: Prof. Rebecca Wade
Molecular and Cellular Modeling Group
Heidelberg Institute for Theoretical Studies (HITS)
Center for Molecular Biology of Heidelberg University (ZMBH)
Interdisciplinary Center for Scientific Computing (IWR)
Heidelberg University, Heidelberg, Germany
Title: Brownian dynamics simulation of the diffusional association of macromolecules
Abstract:
Brownian dynamics (BD) simulations provide a computationally efficient approach to study diffusional association processes. To study protein diffusion and association, we have developed the SDA (Simulation of Diffusional Association) software package [1-3], and its associated webserver, webSDA [4]. In this talk, I will describe the capabilities of SDA and recent methodological advances [5] introduced for studying protein-protein and protein-surface interactions. I will discuss recent applications to studying specific and non-specific protein interactions, including to co-chaperone interactions [6], chromatosome formation [7], protein-gold nanoparticle binding [8], and phosphorylation-dependent allosteric binding [9].
[1] R. R. Gabdoulline, R. C. Wade, Methods, 1998, 14, 329–341.
[2] R. R. Gabdoulline, R. C. Wade, Biophys. J., 1997, 72, 1917–1929.
[3] M. Martinez, N. J. Bruce, J. Romanowska, D. B. Kokh, M. Ozboyaci, X. Yu, M. A. Öztürk, S. Richter, R. C. Wade, J. Comput. Chem., 2015, 36, 1631–1645.
[4] X. Yu, M. Martinez, A. L. Gable, J. C. Fuller, N. J. Bruce, S. Richter, R. C. Wade, Nucleic Acids Res., 2015, 43, W220–W224.
[5] M. Ozboyaci, M. Martinez, R.C. Wade, J Chem Theo Comput 2016, 59, 759-7616.
[6] N. Nillegoda et al. eLife 2017, 6, e24560, Nature 2015, 524, 247-251.
[7] M. A. Öztürk, G.V. Pachov, R.C. Wade, V. Cojocaru. Nucl. Acids Res. 2016, 44, 6599-6613.
[8] M. Ozboyaci, D.B. Kokh, R.C. Wade, Phys Chem Chem Phys 2016, 18, 10191-200.
[9] G. Gdynia et al. Nat. Commun. 2016, 7,10764.
Host: Giorgia Brancolini
Info Rebecca.Wade@h-its.org
Link https://www.h-its.org/en/research/mcm/