caa a22 4500 467938997 CHVBK 20180406153006.0 cr unu---uuuuu 170328e20060201xx s 000 0 eng 10.1007/s10822-006-9039-1 doi (NATIONALLICENCE)springer-10.1007/s10822-006-9039-1 TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations [Elektronische Daten] [Mihaly Mezei, Marta Filizola] Summary: We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs. Springer, 2006 helix geometry nationallicence α-helical proteins nationallicence membrane proteins nationallicence MD nationallicence SIMULAID nationallicence Mezei Mihaly Department of Physiology and Biophysics, Mount Sinai School of Medicine, NYU, One Gustave L. Levy Place, Box 1218, 10029, New York, NY, USA aut Filizola Marta Department of Physiology & Biophysics, Weill Medical College of Cornell University, 1200 York Ave, 10021, New York, NY, USA aut Journal of Computer-Aided Molecular Design Springer Netherlands 20/2(2006-02-01), 97-107 0920-654X 20:2<97 2006 20 10822 https://doi.org/10.1007/s10822-006-9039-1 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10822-006-9039-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Mezei Mihaly Department of Physiology and Biophysics, Mount Sinai School of Medicine, NYU, One Gustave L. Levy Place, Box 1218, 10029, New York, NY, USA aut NATIONALLICENCE 700 1- Filizola Marta Department of Physiology & Biophysics, Weill Medical College of Cornell University, 1200 York Ave, 10021, New York, NY, USA aut NATIONALLICENCE 773 0- Journal of Computer-Aided Molecular Design Springer Netherlands 20/2(2006-02-01), 97-107 0920-654X 20:2<97 2006 20 10822 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer