title: Stretching to understand proteins - a survey of the protein data bank.
abstract: We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps.
authors: Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
authors: Joanna I
authors: JI
authors: Sułkowska
authors: Marek
authors: M
authors: Cieplak
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013314:Stress, Mechanical; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins
references: Nature. 2002 Aug 29;418(6901):998-1002
references: 12198551
references: Nat Struct Biol. 2003 Sep;10(9):731-7
references: 12923573
references: EMBO J. 2003 Oct 1;22(19):5220-9
references: 14517259
references: Biophys J. 2001 Oct;81(4):2344-56
references: 11566804
references: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references: 10592235
references: J Mol Biol. 1999 Jul 2;290(1):253-66
references: 10388571
references: Biophys J. 2006 Feb 15;90(4):L33-5
references: 16361331
references: J Mol Biol. 2005 Nov 25;354(2):497-503
references: 16246362
references: EMBO Rep. 2005 Jan;6(1):46-51
references: 15608615
references: Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):139-44
references: 10618384
references: J Biol Chem. 2002 Mar 29;277(13):11549-58
references: 11799131
references: Biochim Biophys Acta. 2006 Apr;1758(4):537-44
references: 16678120
references: Prog Biophys Mol Biol. 2000;74(1-2):63-91
references: 11106807
references: Biophys J. 2006 Feb 15;90(4):L30-2
references: 16387766
references: J Chem Phys. 2004 Sep 8;121(10):4826-32
references: 15332917
references: Biophys J. 2004 Dec;87(6):3995-4006
references: 15361414
references: Bioinformatics. 1999 Apr;15(4):327-32
references: 10320401
references: Fold Des. 1997;2(1):1-22
references: 9080195
references: Protein Sci. 2002 Oct;11(10):2351-61
references: 12237457
references: Nat Struct Mol Biol. 2004 Jan;11(1):81-5
references: 14718927
references: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1565-70
references: 11171991
references: J Chem Phys. 2005 Feb 1;122(5):54906
references: 15740352
references: J Mol Biol. 1999 Feb 19;286(2):553-61
references: 9973570
references: Nature. 2006 Mar 9;440(7081):246-9
references: 16415852
references: Biopolymers. 1981 May;20(5):1013-31
references: 7225529
references: FEBS Lett. 2000 Jul 7;476(3):124-8
references: 10913598
references: J Biol Chem. 2004 Apr 16;279(16):16410-6
references: 14761982
references: Proteins. 2004 Aug 1;56(2):285-97
references: 15211512
references: J Struct Biol. 2002 Jan-Feb;137(1-2):248-58
references: 12064950
references: Biophys J. 2003 Jan;84(1):533-44
references: 12524305
references: Science. 2005 Sep 23;309(5743):2057-60
references: 16179479
references: Structure. 1997 Aug 15;5(8):1093-108
references: 9309224
references: Biophys J. 2005 Jul;89(1):506-19
references: 15863479
references: J Chem Phys. 2006 Oct 28;125(16):164903
references: 17092135
references: Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6527-31
references: 10823913
references: Biophys J. 2000 Apr;78(4):1965-78
references: 10733975
references: Biophys J. 2003 Jan;84(1):475-88
references: 12524300
references: Nat Struct Biol. 2003 Sep;10(9):738-43
references: 12923571
references: Science. 1992 Nov 6;258(5084):987-91
references: 1279805
references: J Mol Biol. 2002 May 31;319(2):433-47
references: 12051919
references: J Mol Biol. 2000 May 19;298(5):937-53
references: 10801360
references: Biophys J. 2006 Jan 1;90(1):287-97
references: 16214858
references: Biophys J. 1998 Aug;75(2):662-71
references: 9675168
references: J Mol Biol. 2005 Jan 28;345(4):817-26
references: 15588828