TMM@: A web application for the analysis of transmembrane helix mobility

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Skjaerven, Lars ^a   Jonassen, Inge ^a   Reuter, Nathalie ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

MACROMOLECULAR SYSTEMS; NORMAL MODE ANALYSIS; TRANS-MEMBRANE PROTEINS; TRANSMEMBRANE CHANNELS; TRANSMEMBRANE HELICES; VIBRATIONAL NORMAL MODES; WEB APPLICATION; WEB APPLICATIONS;

CELL MEMBRANES; CYTOLOGY; TOOLS; WORLD WIDE WEB;

PROTEINS;

MEMBRANE PROTEIN;

ALPHA HELIX; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; INTRACELLULAR TRANSPORT; ION TRANSPORT; MEMBRANE CHANNEL; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTEIN TRANSPORT; SIGNAL TRANSDUCTION; WEB BROWSER; ALGORITHM; CELL MEMBRANE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER SIMULATION; INTERNET; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; ULTRASTRUCTURE;

ALGORITHMS; CELL MEMBRANE; COMPUTER GRAPHICS; COMPUTER SIMULATION; INTERNET; MEMBRANE PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 34548135296     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-232     Document Type: Article

References (30)

1. Curran AR Engelman DM Sequence motifs, polar interactions and conformational changes in helical membrane proteins Curr Opin Struct Biol 2003 13 4 412-417 10.1016/S0959-440X(03)00102-7 12948770
2. Sukharev S Anishkin A Mechanosensitive channels: What can we learn from 'simple' model systems? Trends Neurosci 2004 27 6 345-351 10.1016/ j.tins.2004.04.006 15165739
3. Toyoshima C Nomura H Tsuda T Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues Nature 2004 432 7015 361-368 10.1038/nature02981 15448704
4. Hayward S Normal mode analysis of biological molecules Computational biochemistry and biophysics New-York, Marcel Dekker, Inc. Becker OM, MacKerell AD, Roux B, Watanabe M 2001 153-168
5. Levitt M Sander C Stern PS Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme J Mol Biol 1985 181 3 423-447 10.1016/0022-2836(85)90230-X 2580101
6. Marques O Sanejouand YH Hinge-bending motion in citrate synthase arising from normal mode calculations Proteins 1995 23 4 557-560 10.1002/ prot.340230410 8749851
7. Mouawad L Perahia D Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary T-like, quaternary R-like intermediate structures J Mol Biol 1996 258 2 393-410 10.1006/jmbi.1996.0257 8627633
8. Hayward S Kitao A Berendsen HJ Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme Proteins 1997 27 3 425-437 10.1002/ (SICI)1097-0134(199703)27:3<425::AID-PROT10>3.0.CO;2-N 9094744
9. Ma J Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes Structure (Camb) 2005 13 3 373-380 10.1016/j.str.2005.02.002
10. Suhre K Sanejouand YH ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Res 2004 32 Web Server issue W610-4 441506 15215461 10.1093/nar/gkh368
11. Echols N Milburn D Gerstein M MolMovDB: Analysis and visualization of conformational change and structural flexibility Nucleic Acids Res 2003 31 1 478-482 165551 12520056 10.1093/nar/gkg104
12. Wako H Kato M Endo S ProMode: A database of normal mode analyses on protein molecules with a full-atom model Bioinformatics 2004 20 13 2035-2043 10.1093/bioinformatics/bth197 15059828
13. Hollup SM Salensminde G Reuter N WEBnm" a web application for normal mode analyses of proteins BMC Bioinformatics 2005 6 1 52 1274249 15762993 10.1186/1471-2105-6-52
14. Yang LW Liu X Jursa CJ Holliman M Rader AJ Karimi HA Bahar I iGNM: A database of protein functional motions based on Gaussian Network Model Bioinformatics 2005 21 13 2978-2987 1752228 15860562 10.1093/ bioinformatics/bti469
15. Delarue M Lindahl E Normal mode calculation and visualisation using Pymol 2004 http://lorentz.immstr.pasteur.fr/nma/
16. Valadie H Lacapere JJ Sanejouand YH Etchebest C Dynamical properties of the MscL of Escherichia coli: A normal mode analysis J Mol Biol 2003 332 3 657-674 10.1016/S0022-2836(03)00851-9 12963374
17. Shrivastava IH Bahar I Common mechanism of pore opening shared by five different potassium channels Biophys J 2006 90 11 3929-3940 1459499 16533848 10.1529/biophysj.105.080093
18. Reuter N Hinsen K Lacapere JJ Transconformations of the SERCA1 Ca-ATPase: A normal mode study Biophys J 2003 85 4 2186-2197 1303445 14507684
19. Zope Open Source web application server. http://www.zope.org/
20. Saelensminde G The Biaz application server 2003 http://www.bioinfo.no/ tools/Biaz
21. Hinsen K The Molecular Modeling Toolkit: A new approach to molecular simulations J Comput Chem 2000 21 2 79-85 10.1002/ (SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B
22. R Copyright (C) 1989, 1991 Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA http://www.r-project.org/
23. Moreira W Warnes GR RPy 2003 http://rpy.sourceforge.net/
24. Gezelter JD Jmol - http://jmol.sourceforge.net/ 2006 http:// jmol.sourceforge.net/ 16821904
25. Humphrey W Dalke A Schulten K VMD - Visual Molecular Dynamics J Molec Graphics 1996 14 1 33-38 10.1016/0263-7855(96)00018-5
26. Hinsen K Analysis of domain motions by approximate normal mode calculations Proteins 1998 33 417-429 10.1002/ (SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8 9829700
27. Hinsen K Petrescu AJ Dellerue S Bellissent-Funel MC Kneller GR Harmonicity in slow protein dynamics Chem Phys 2000 261 25-37 10.1016/ S0301-0104(00)00222-6
28. Kabsch W Sander C Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983 22 12 2577-2637 10.1002/bip.360221211 6667333
29. Song G Jernigan RL An enhanced elastic network model to represent the motions of domain-swapped proteins Proteins 2006 63 1 197-209 10.1002/ prot.20836 16447281
30. Toyoshima C Mizutani T Crystal structure of the calcium pump with a bound ATP analogue Nature 2004 430 6999 529-535 10.1038/nature02680 15229613