Paper Citing NAMD - Abstract
Genchev, Georgi Z.; Kaellberg, Morten; Guersoy, Gamze; Mittal, Anuradha; Dubey, Lalit; Perisic, Ognjen; Feng, Gang; Langlois, Robert; Lu, Hui
Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics
CELL BIOCHEMISTRY AND BIOPHYSICS, 55:141-152, DEC 2009
Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.
